1
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Zheng Y, Zhang Y, Li X, Liu L. Proof of ssDNA degraded from dsDNA for ET recombination. Biochem Biophys Rep 2024; 39:101750. [PMID: 39035021 PMCID: PMC11257833 DOI: 10.1016/j.bbrep.2024.101750] [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: 03/11/2024] [Accepted: 06/04/2024] [Indexed: 07/23/2024] Open
Abstract
The widely used ET recombination requires an ssDNA product degraded by Rac phage protein E588 from dsDNA for strand invasion. However, proof of the ssDNA product is still elusive. The study provided three levels of proof sequentially. The probable ssDNAs degraded by E588 from the fluorescent plus-, minus-, or double-stranded dsDNA pET28a-xylanase exhibited a half fluorescence intensity of the corresponding dsDNAs, equivalent to the E588 degradation nucleotides half that of the total nucleotides degraded from the corresponding dsDNA. The ssDNA product degraded by E588 from the fluorescent minus-stranded dsDNA was confirmed by gradient gel-electrophoresis and two nuclease degradation reactions. Degraded by E588 from the dsDNA pET28a-xylanase that had a phosphorothioated plus-stranded 5'-terminus, the plus-stranded ssDNA product was separated via gel electrophoresis and recovered via a DNAclean kit. The recovered ssDNA product was proven to have intact 5'- and 3'-ends by DNA sequencing analysis. This study provides a solid foundation for the mechanism of ssDNA invasion.
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Affiliation(s)
- Yuanxia Zheng
- Life Science College, Henan Agricultural University, Zhengzhou, 450046, China
| | - Yi Zhang
- Life Science College, Henan Agricultural University, Zhengzhou, 450046, China
| | - Xuegang Li
- Life Science College, Henan Agricultural University, Zhengzhou, 450046, China
| | - Liangwei Liu
- Life Science College, Henan Agricultural University, Zhengzhou, 450046, China
- The Key Laboratory of Enzyme Engineering of Agricultural Microbiology, Ministry of Agriculture, Zhengzhou, 450046, 218 Pingan Road, China
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2
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Blanch-Asensio A, Grandela C, Mummery CL, Davis RP. STRAIGHT-IN: a platform for rapidly generating panels of genetically modified human pluripotent stem cell lines. Nat Protoc 2024:10.1038/s41596-024-01039-2. [PMID: 39179886 DOI: 10.1038/s41596-024-01039-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 06/11/2024] [Indexed: 08/26/2024]
Abstract
Targeted integration of large DNA cargoes (>10 kb) or genomic replacements in mammalian cells, such as human pluripotent stem cells (hPS cells), remains challenging. Here we describe a platform termed serine and tyrosine recombinase-assisted integration of genes for high-throughput investigation (STRAIGHT-IN) to circumvent this. First, a landing pad cassette is precisely inserted or used to replace specific genomic regions. The site-specific integrase Bxb1 then enables DNA constructs, including those >50 kb, to be integrated into the genome, while Cre recombinase excises auxiliary DNA sequences to prevent postintegrative silencing. Using a strategy whereby the positive selection marker is only expressed if the donor plasmid carrying the payload is correctly targeted, we can obtain 100% enrichment for cells containing the DNA payload. Procedures for expressing Cre efficiently also mean that a clonal isolation step is no longer essential to derive the required genetically modified hPS cells containing the integrated DNA, potentially reducing clonal variability. Furthermore, STRAIGHT-IN facilitates rapid and multiplexed generation of genetically matched hPS cells when multiple donor plasmids are delivered simultaneously. STRAIGHT-IN has various applications, which include integrating complex genetic circuits for synthetic biology, as well as creating panels of hPS cells lines containing, as necessary, hundreds of disease-linked variants for disease modeling and drug discovery. After establishing the hPS cell line containing the landing pad, the entire procedure, including donor plasmid synthesis, takes 1.5-3 months, depending on whether single or multiple DNA payloads are integrated. This protocol only requires the researcher to be skilled in molecular biology and standard cell culture techniques.
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Affiliation(s)
- Albert Blanch-Asensio
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, the Netherlands
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, the Netherlands
| | - Catarina Grandela
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, the Netherlands
| | - Christine L Mummery
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, the Netherlands
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, the Netherlands
| | - Richard P Davis
- Department of Anatomy and Embryology, Leiden University Medical Center, Leiden, the Netherlands.
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden University Medical Center, Leiden, the Netherlands.
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3
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He H, Zheng W, Xiao S, Gong L, Li H, Zhou K, Zhang L, Tu Q, Zhu YZ, Zhang Y. Deciphering the Nitrogen Fixation Gene Cluster in Vibrio natriegens: A Study on Optimized Expression and Application of Nitrogenase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:12618-12629. [PMID: 38778776 DOI: 10.1021/acs.jafc.4c01232] [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: 05/25/2024]
Abstract
Microbial nitrogen fixation presents a viable alternative to chemical fertilizers, yet the limited colonization and specificity of naturally occurring nitrogen-fixing microorganisms present significant challenges to their widespread application. In this study, we identified a nitrogen fixation gene cluster (VNnif) in Vibrio natriegens (VN) and tested its nitrogenase activity through the acetylene reduction assay. We investigated the potential utilization of nitrogenase by incorporating the nitrogenase gene cluster from VN into plant growth-promoting rhizosphere bacteria Pseudomonas protegens CHA0 and enhancing its activity to 48.16 nmol C2H2/mg/h through promoter replacement and cluster rearrangement. The engineered strain CHA0-PVNnif was found to positively impact the growth of Arabidopsis thaliana col-0 and Triticum aestivum L. (wheat). This study expanded the role of plant growth-promoting rhizobacteria (PGPR) and provided a research foundation for enhancing nitrogenase activity.
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Affiliation(s)
- Haocheng He
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Weijin Zheng
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- College of Life and Geographic Sciences, Kashi University, Kashi 844099, China
| | - Shuai Xiao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Liang Gong
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - He Li
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau SAR 999078, China
| | - Kexuan Zhou
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau SAR 999078, China
| | - Letian 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
- State Key Lab of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Qiang Tu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yi Zhun Zhu
- School of Pharmacy, Faculty of Medicine, Macau University of Science and Technology, Macau SAR 999078, China
- State Key Lab of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - 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
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Yang SNN, Haritos V, Kertesz MA, Coleman NV. A novel soluble di-iron monooxygenase from the soil bacterium Solimonas soli. Environ Microbiol 2024; 26:e16567. [PMID: 38233213 DOI: 10.1111/1462-2920.16567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 12/12/2023] [Indexed: 01/19/2024]
Abstract
Soluble di-iron monooxygenase (SDIMO) enzymes enable insertion of oxygen into diverse substrates and play significant roles in biogeochemistry, bioremediation and biocatalysis. An unusual SDIMO was detected in an earlier study in the genome of the soil organism Solimonas soli, but was not characterized. Here, we show that the S. soli SDIMO is part of a new clade, which we define as 'Group 7'; these share a conserved gene organization with alkene monooxygenases but have only low amino acid identity. The S. soli genes (named zmoABCD) could be functionally expressed in Pseudomonas putida KT2440 but not in Escherichia coli TOP10. The recombinants made epoxides from C2 C8 alkenes, preferring small linear alkenes (e.g. propene), but also epoxidating branched, carboxylated and chlorinated substrates. Enzymatic epoxidation of acrylic acid was observed for the first time. ZmoABCD oxidised the organochlorine pollutants vinyl chloride (VC) and cis-1,2-dichloroethene (cDCE), with the release of inorganic chloride from VC but not cDCE. The original host bacterium S. soli could not grow on any alkenes tested but grew well on phenol and n-octane. Further work is needed to link ZmoABCD and the other Group 7 SDIMOs to specific physiological and ecological roles.
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Affiliation(s)
- Sui Nin Nicholas Yang
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Victoria Haritos
- Department of Chemical and Biological Engineering, Monash University, Melbourne, Victoria, Australia
| | - Michael A Kertesz
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
| | - Nicholas V Coleman
- School of Life and Environmental Sciences, University of Sydney, Camperdown, New South Wales, Australia
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Beganovic S, Rückert-Reed C, Sucipto H, Shu W, Gläser L, Patschkowski T, Struck B, Kalinowski J, Luzhetskyy A, Wittmann C. Systems biology of industrial oxytetracycline production in Streptomyces rimosus: the secrets of a mutagenized hyperproducer. Microb Cell Fact 2023; 22:222. [PMID: 37898787 PMCID: PMC10612213 DOI: 10.1186/s12934-023-02215-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 09/26/2023] [Indexed: 10/30/2023] Open
Abstract
BACKGROUND Oxytetracycline which is derived from Streptomyces rimosus, inhibits a wide range of bacteria and is industrially important. The underlying biosynthetic processes are complex and hinder rational engineering, so industrial manufacturing currently relies on classical mutants for production. While the biochemistry underlying oxytetracycline synthesis is known to involve polyketide synthase, hyperproducing strains of S. rimosus have not been extensively studied, limiting our knowledge on fundamental mechanisms that drive production. RESULTS In this study, a multiomics analysis of S. rimosus is performed and wild-type and hyperproducing strains are compared. Insights into the metabolic and regulatory networks driving oxytetracycline formation were obtained. The overproducer exhibited increased acetyl-CoA and malonyl CoA supply, upregulated oxytetracycline biosynthesis, reduced competing byproduct formation, and streamlined morphology. These features were used to synthesize bhimamycin, an antibiotic, and a novel microbial chassis strain was created. A cluster deletion derivative showed enhanced bhimamycin production. CONCLUSIONS This study suggests that the precursor supply should be globally increased to further increase the expression of the oxytetracycline cluster while maintaining the natural cluster sequence. The mutagenized hyperproducer S. rimosus HP126 exhibited numerous mutations, including large genomic rearrangements, due to natural genetic instability, and single nucleotide changes. More complex mutations were found than those typically observed in mutagenized bacteria, impacting gene expression, and complicating rational engineering. Overall, the approach revealed key traits influencing oxytetracycline production in S. rimosus, suggesting that similar studies for other antibiotics could uncover general mechanisms to improve production.
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Affiliation(s)
- Selma Beganovic
- Institute of Systems Biotechnology, Saarland University, Campus A1 5, 66123, Saarbrücken, Germany
| | | | - Hilda Sucipto
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Wei Shu
- Institute of Systems Biotechnology, Saarland University, Campus A1 5, 66123, Saarbrücken, Germany
| | - Lars Gläser
- Institute of Systems Biotechnology, Saarland University, Campus A1 5, 66123, Saarbrücken, Germany
| | | | - Ben Struck
- Centre for Biotechnology, Bielefeld University, Bielefeld, Germany
| | - Jörn Kalinowski
- Centre for Biotechnology, Bielefeld University, Bielefeld, Germany
| | | | - Christoph Wittmann
- Institute of Systems Biotechnology, Saarland University, Campus A1 5, 66123, Saarbrücken, Germany. *
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6
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Chen H, Bai X, Sun T, Wang X, Zhang Y, Bian X, Zhou H. The Genomic-Driven Discovery of Glutarimide-Containing Derivatives from Burkholderia gladioli. Molecules 2023; 28:6937. [PMID: 37836780 PMCID: PMC10574677 DOI: 10.3390/molecules28196937] [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: 08/04/2023] [Revised: 09/20/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Glutarimide-containing polyketides exhibiting potent antitumor and antimicrobial activities were encoded via conserved module blocks in various strains that favor the genomic mining of these family compounds. The bioinformatic analysis of the genome of Burkholderia gladioli ATCC 10248 showed a silent trans-AT PKS biosynthetic gene cluster (BGC) on chromosome 2 (Chr2C8), which was predicted to produce new glutarimide-containing derivatives. Then, the silent polyketide synthase gene cluster was successfully activated via in situ promoter insertion and heterologous expression. As a result, seven glutarimide-containing analogs, including five new ones, gladiofungins D-H (3-7), and two known gladiofungin A/gladiostatin (1) and 2 (named gladiofungin C), were isolated from the fermentation of the activated mutant. Their structures were elucidated through the analysis of HR-ESI-MS and NMR spectroscopy. The structural diversities of gladiofungins may be due to the degradation of the butenolide group in gladiofungin A (1) during the fermentation and extraction process. Bioactivity screening showed that 2 and 4 had moderate anti-inflammatory activities. Thus, genome mining combined with promoter engineering and heterologous expression were proved to be effective strategies for the pathway-specific activation of the silent BGCs for the directional discovery of new natural products.
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Affiliation(s)
- Hanna Chen
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (H.C.); (X.B.); (T.S.); (X.W.)
- School of Medicine, Linyi University, Shuangling Road, Linyi 276000, China
| | - Xianping Bai
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (H.C.); (X.B.); (T.S.); (X.W.)
| | - Tao Sun
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (H.C.); (X.B.); (T.S.); (X.W.)
| | - Xingyan Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (H.C.); (X.B.); (T.S.); (X.W.)
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (H.C.); (X.B.); (T.S.); (X.W.)
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xiaoying Bian
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (H.C.); (X.B.); (T.S.); (X.W.)
| | - Haibo Zhou
- Helmholtz International Lab for Anti-Infectives, Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, China; (H.C.); (X.B.); (T.S.); (X.W.)
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7
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Zheng W, Xia Y, Wang X, Gao S, Zhou D, Ravichandran V, Jiang C, Tu Q, Yin Y, Zhang Y, Fu J, Li R, Yin J. Precise genome engineering in Pseudomonas using phage-encoded homologous recombination and the Cascade-Cas3 system. Nat Protoc 2023; 18:2642-2670. [PMID: 37626246 DOI: 10.1038/s41596-023-00856-1] [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: 09/17/2022] [Accepted: 05/11/2023] [Indexed: 08/27/2023]
Abstract
A lack of generic and effective genetic manipulation methods for Pseudomonas has restricted fundamental research and utilization of this genus for biotechnology applications. Phage-encoded homologous recombination (PEHR) is an efficient tool for bacterial genome engineering. This PEHR system is based on a lambda Red-like operon (BAS) from Pseudomonas aeruginosa phage Ab31 and a Rac bacteriophage RecET-like operon (Rec-TEPsy) from P. syringae pv. syringae B728a and also contains exogenous elements, including the RecBCD inhibitor (Redγ or Pluγ) or single-stranded DNA-binding protein (SSB), that were added to enhance the PEHR recombineering efficiency. To solve the problem of false positives in Pseudomonas editing with the PEHR system, the processive enzyme Cas3 with a minimal Type I-C Cascade-based system was combined with PEHR. This protocol describes the utilization of a Pseudomonas-specific PEHR-Cas3 system that was designed to universally and proficiently modify the genomes of Pseudomonas species. The pipeline uses standardized cassettes combined with the concerted use of SacB counterselection and Cre site-specific recombinase for markerless or seamless genome modification, in association with vectors that possess the selectively replicating template R6K to minimize recombineering background. Compared with the traditional allelic exchange editing method, the PEHR-Cas3 system does not need to construct suicide plasmids carrying long homologous arms, thus simplifying the experimental procedure and shortening the traceless editing period. Compared with general editing systems based on phage recombinases, the PEHR-Cas3 system can effectively improve the screening efficiency of mutants using the cutting ability of Cas3 protein. The entire procedure requires ~12 days.
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Affiliation(s)
- Wentao Zheng
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Yandong Xia
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Sciences, Hunan Normal University, Changsha, China
- College of Life Science and Technology, Key Laboratory of National Forestry and Grassland Administration on Control of Artificial Forest Diseases and Pests in South China, Hunan Provincial Key Laboratory for Control of Forest Diseases and Pests, Key Laboratory for Non-wood Forest Cultivation and Conservation of Ministry of Education, Central South University of Forestry and Technology, Changsha, China
| | - Xue Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Shiqing Gao
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Diao Zhou
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Sciences, Hunan Normal University, Changsha, China
| | | | - Chanjuan Jiang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Qiang Tu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 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
| | - Yulong Yin
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 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
| | - Jun Fu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
| | - Ruijuan Li
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China.
| | - Jia Yin
- Hunan Provincial Key Laboratory of Animal Intestinal Function and Regulation, Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, College of Life Sciences, Hunan Normal University, Changsha, China.
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Collective cell migration during optic cup formation features changing cell-matrix interactions linked to matrix topology. Curr Biol 2022; 32:4817-4831.e9. [PMID: 36208624 DOI: 10.1016/j.cub.2022.09.034] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 07/28/2022] [Accepted: 09/16/2022] [Indexed: 11/22/2022]
Abstract
Cell migration is crucial for organismal development and shapes organisms in health and disease. Although a lot of research has revealed the role of intracellular components and extracellular signaling in driving single and collective cell migration, the influence of physical properties of the tissue and the environment on migration phenomena in vivo remains less explored. In particular, the role of the extracellular matrix (ECM), which many cells move upon, is currently unclear. To overcome this gap, we use zebrafish optic cup formation, and by combining novel transgenic lines and image analysis pipelines, we study how ECM properties influence cell migration in vivo. We show that collectively migrating rim cells actively move over an immobile extracellular matrix. These cell movements require cryptic lamellipodia that are extended in the direction of migration. Quantitative analysis of matrix properties revealed that the topology of the matrix changes along the migration path. These changes in matrix topologies are accompanied by changes in the dynamics of cell-matrix interactions. Experiments and theoretical modeling suggest that matrix porosity could be linked to efficient migration. Indeed, interfering with matrix topology by increasing its porosity results in a loss of cryptic lamellipodia, less-directed cell-matrix interactions, and overall inefficient migration. Thus, matrix topology is linked to the dynamics of cell-matrix interactions and the efficiency of directed collective rim cell migration during vertebrate optic cup morphogenesis.
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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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10
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Expression of Cyanobacterial Biosynthetic Gene Clusters in Escherichia coli. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2489:315-332. [PMID: 35524058 DOI: 10.1007/978-1-0716-2273-5_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Cyanobacteria represent an attractive source of natural bioactive compounds, ranging from sunscreens to cancer treatments. While many biosynthetic gene clusters (BGCs) that encode cyanobacterial natural products are known, the slow growth and lack of genetic tools in the native producers hampers their modification, characterization, and large-scale production. By engineering heterologous hosts for the expression of cyanobacterial BGCs, sufficient material can be produced for research or industry. Although several hosts have been evaluated for the expression of cyanobacterial natural products, this work details the process of expressing BGCs in Escherichia coli via promoter exchange.
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11
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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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12
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MLL1 is required for maintenance of intestinal stem cells. PLoS Genet 2021; 17:e1009250. [PMID: 34860830 PMCID: PMC8641872 DOI: 10.1371/journal.pgen.1009250] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 10/30/2021] [Indexed: 12/12/2022] Open
Abstract
Epigenetic mechanisms are gatekeepers for the gene expression patterns that establish and maintain cellular identity in mammalian development, stem cells and adult homeostasis. Amongst many epigenetic marks, methylation of histone 3 lysine 4 (H3K4) is one of the most widely conserved and occupies a central position in gene expression. Mixed lineage leukemia 1 (MLL1/KMT2A) is the founding mammalian H3K4 methyltransferase. It was discovered as the causative mutation in early onset leukemia and subsequently found to be required for the establishment of definitive hematopoiesis and the maintenance of adult hematopoietic stem cells. Despite wide expression, the roles of MLL1 in non-hematopoietic tissues remain largely unexplored. To bypass hematopoietic lethality, we used bone marrow transplantation and conditional mutagenesis to discover that the most overt phenotype in adult Mll1-mutant mice is intestinal failure. MLL1 is expressed in intestinal stem cells (ISCs) and transit amplifying (TA) cells but not in the villus. Loss of MLL1 is accompanied by loss of ISCs and a differentiation bias towards the secretory lineage with increased numbers and enlargement of goblet cells. Expression profiling of sorted ISCs revealed that MLL1 is required to promote expression of several definitive intestinal transcription factors including Pitx1, Pitx2, Foxa1, Gata4, Zfp503 and Onecut2, as well as the H3K27me3 binder, Bahcc1. These results were recapitulated using conditional mutagenesis in intestinal organoids. The stem cell niche in the crypt includes ISCs in close association with Paneth cells. Loss of MLL1 from ISCs promoted transcriptional changes in Paneth cells involving metabolic and stress responses. Here we add ISCs to the MLL1 repertoire and observe that all known functions of MLL1 relate to the properties of somatic stem cells, thereby highlighting the suggestion that MLL1 is a master somatic stem cell regulator.
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Rational construction of genome-reduced Burkholderiales chassis facilitates efficient heterologous production of natural products from proteobacteria. Nat Commun 2021; 12:4347. [PMID: 34301933 PMCID: PMC8302735 DOI: 10.1038/s41467-021-24645-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 06/29/2021] [Indexed: 02/06/2023] Open
Abstract
Heterologous expression of biosynthetic gene clusters (BGCs) avails yield improvements and mining of natural products, but it is limited by lacking of more efficient Gram-negative chassis. The proteobacterium Schlegelella brevitalea DSM 7029 exhibits potential for heterologous BGC expression, but its cells undergo early autolysis, hindering further applications. Herein, we rationally construct DC and DT series genome-reduced S. brevitalea mutants by sequential deletions of endogenous BGCs and the nonessential genomic regions, respectively. The DC5 to DC7 mutants affect growth, while the DT series mutants show improved growth characteristics with alleviated cell autolysis. The yield improvements of six proteobacterial natural products and successful identification of chitinimides from Chitinimonas koreensis via heterologous expression in DT mutants demonstrate their superiority to wild-type DSM 7029 and two commonly used Gram-negative chassis Escherichia coli and Pseudomonas putida. Our study expands the panel of Gram-negative chassis and facilitates the discovery of natural products by heterologous expression.
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14
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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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15
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Zheng W, Wang X, Chen Y, Dong Y, Zhou D, Liu R, Zhou H, Bian X, Wang H, Tu Q, Ravichandran V, Zhang Y, Li A, Fu J, Yin J. Recombineering facilitates the discovery of natural product biosynthetic pathways in Pseudomonas parafulva. Biotechnol J 2021; 16:e2000575. [PMID: 33484238 DOI: 10.1002/biot.202000575] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 01/15/2021] [Accepted: 01/21/2021] [Indexed: 11/07/2022]
Abstract
Microbial natural products among other functions they play a vital role in the disease prevention in humans, animals and plants. Pseudomonas parafulva CRS01-1 is a broad-spectrum antagonistic bacterium present in plants. However, no natural products have been isolated from this strain till date. Corresponding biosynthetic gene clusters to natural products is an effective method for bioprospecting, for which, genome manipulation tools are essential. We previously developed Pseudomonas-specific phage-derived homologous recombination systems for genetic engineering in four Pseudomonas species. Herein, we report the application of these recombineering systems in Pseudomonas parafulva CRS01-1, along with structural elucidation and bioactivity evaluation of natural products. The Pseudomonas recombineering toolbox established before in different four species is efficient for genome mining and bioactive metabolite discovery from more distant species.
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Affiliation(s)
- Wentao Zheng
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Xue Wang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Yuwei Chen
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, People's Republic of China
| | - Yachao Dong
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, People's Republic of China
| | - Diao Zhou
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, People's Republic of China
| | - Ruxin Liu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Haibo Zhou
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Xiaoying Bian
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Hailong Wang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Qiang Tu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Vinothkannan Ravichandran
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Youming Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Aiying Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Jun Fu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People's Republic of China
| | - Jia Yin
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, Changsha, People's Republic of China
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16
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Caldwell BJ, Norris A, Zakharova E, Smith CE, Wheat CT, Choudhary D, Sotomayor M, Wysocki VH, Bell CE. Oligomeric complexes formed by Redβ single strand annealing protein in its different DNA bound states. Nucleic Acids Res 2021; 49:3441-3460. [PMID: 33693865 PMCID: PMC8034648 DOI: 10.1093/nar/gkab125] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 02/09/2021] [Accepted: 03/02/2021] [Indexed: 02/06/2023] Open
Abstract
Redβ is a single strand annealing protein from bacteriophage λ that binds loosely to ssDNA, not at all to pre-formed dsDNA, but tightly to a duplex intermediate of annealing. As viewed by electron microscopy, Redβ forms oligomeric rings on ssDNA substrate, and helical filaments on the annealed duplex intermediate. However, it is not clear if these are the functional forms of the protein in vivo. We have used size-exclusion chromatography coupled with multi-angle light scattering, analytical ultracentrifugation and native mass spectrometry (nMS) to characterize the size of the oligomers formed by Redβ in its different DNA-bound states. The nMS data, which resolve species with the highest resolution, reveal that Redβ forms an oligomer of 12 subunits in the absence of DNA, complexes ranging from 4 to 14 subunits on 38-mer ssDNA, and a much more distinct and stable complex of 11 subunits on 38-mer annealed duplex. We also measure the concentration of Redβ in cells active for recombination and find it to range from 7 to 27 μM. Collectively, these data provide new insights into the dynamic nature of the complex on ssDNA, and the more stable and defined complex on annealed duplex.
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Affiliation(s)
- Brian J Caldwell
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.,Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Andrew Norris
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Ekaterina Zakharova
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Christopher E Smith
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.,Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Carter T Wheat
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.,Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA
| | - Deepanshu Choudhary
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Marcos Sotomayor
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Vicki H Wysocki
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Charles E Bell
- Ohio State Biochemistry Program, The Ohio State University, Columbus, OH 43210, USA.,Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210, USA.,Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
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17
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Gudiño V, Pohl SÖG, Billard CV, Cammareri P, Bolado A, Aitken S, Stevenson D, Hall AE, Agostino M, Cassidy J, Nixon C, von Kriegsheim A, Freile P, Popplewell L, Dickson G, Murphy L, Wheeler A, Dunlop M, Din F, Strathdee D, Sansom OJ, Myant KB. RAC1B modulates intestinal tumourigenesis via modulation of WNT and EGFR signalling pathways. Nat Commun 2021; 12:2335. [PMID: 33879799 PMCID: PMC8058071 DOI: 10.1038/s41467-021-22531-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 03/16/2021] [Indexed: 02/07/2023] Open
Abstract
Current therapeutic options for treating colorectal cancer have little clinical efficacy and acquired resistance during treatment is common, even following patient stratification. Understanding the mechanisms that promote therapy resistance may lead to the development of novel therapeutic options that complement existing treatments and improve patient outcome. Here, we identify RAC1B as an important mediator of colorectal tumourigenesis and a potential target for enhancing the efficacy of EGFR inhibitor treatment. We find that high RAC1B expression in human colorectal cancer is associated with aggressive disease and poor prognosis and deletion of Rac1b in a mouse colorectal cancer model reduces tumourigenesis. We demonstrate that RAC1B interacts with, and is required for efficient activation of the EGFR signalling pathway. Moreover, RAC1B inhibition sensitises cetuximab resistant human tumour organoids to the effects of EGFR inhibition, outlining a potential therapeutic target for improving the clinical efficacy of EGFR inhibitors in colorectal cancer.
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Affiliation(s)
- Victoria Gudiño
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
- Inflammatory Bowel Disease Unit, Department of Gastroenterology, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) - CIBEREHD, Barcelona, Spain
| | - Sebastian Öther-Gee Pohl
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Caroline V Billard
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Patrizia Cammareri
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Alfonso Bolado
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Stuart Aitken
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - David Stevenson
- Cancer Research UK Beatson Institute, Garscube Estate, Bearsden, Glasgow, G61 1BD, UK
| | - Adam E Hall
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Mark Agostino
- School of Pharmacy and Biomedical Sciences, Curtin Health and Innovation Research Institute, Curtin University, Perth, WA, 6845, Australia
- Curtin Institute for Computation, Curtin University, Perth, WA, 6845, Australia
| | - John Cassidy
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK
| | - Colin Nixon
- Cancer Research UK Beatson Institute, Garscube Estate, Bearsden, Glasgow, G61 1BD, UK
| | - Alex von Kriegsheim
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Paz Freile
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Linda Popplewell
- School of Biological Sciences, Royal Holloway - University of London, Egham, Surrey, TW20 0EX, UK
| | - George Dickson
- School of Biological Sciences, Royal Holloway - University of London, Egham, Surrey, TW20 0EX, UK
| | - Laura Murphy
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Ann Wheeler
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Malcolm Dunlop
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Farhat Din
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
- MRC Human Genetics Unit, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK
| | - Douglas Strathdee
- Cancer Research UK Beatson Institute, Garscube Estate, Bearsden, Glasgow, G61 1BD, UK
| | - Owen J Sansom
- Cancer Research UK Beatson Institute, Garscube Estate, Bearsden, Glasgow, G61 1BD, UK
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Bearsden, Glasgow, G61 1QH, UK
| | - Kevin B Myant
- Cancer Research UK Edinburgh Centre, MRC Institute of Genetics & Molecular Medicine, The University of Edinburgh, Western General Hospital, Edinburgh, EH4 2XU, UK.
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18
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Ashokkumar D, Zhang Q, Much C, Bledau AS, Naumann R, Alexopoulou D, Dahl A, Goveas N, Fu J, Anastassiadis K, Stewart AF, Kranz A. MLL4 is required after implantation, whereas MLL3 becomes essential during late gestation. Development 2020; 147:dev186999. [PMID: 32439762 DOI: 10.1242/dev.186999] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 04/24/2020] [Indexed: 12/26/2022]
Abstract
Methylation of histone 3 lysine 4 (H3K4) is a major epigenetic system associated with gene expression. In mammals there are six H3K4 methyltransferases related to yeast Set1 and fly Trithorax, including two orthologs of fly Trithorax-related: MLL3 and MLL4. Exome sequencing has documented high frequencies of MLL3 and MLL4 mutations in many types of human cancer. Despite this emerging importance, the requirements of these paralogs in mammalian development have only been incompletely reported. Here, we examined the null phenotypes to establish that MLL3 is first required for lung maturation, whereas MLL4 is first required for migration of the anterior visceral endoderm that initiates gastrulation in the mouse. This collective cell migration is preceded by a columnar-to-squamous transition in visceral endoderm cells that depends on MLL4. Furthermore, Mll4 mutants display incompletely penetrant, sex-distorted, embryonic haploinsufficiency and adult heterozygous mutants show aspects of Kabuki syndrome, indicating that MLL4 action, unlike MLL3, is dosage dependent. The highly specific and discordant functions of these paralogs in mouse development argues against their action as general enhancer factors.
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Affiliation(s)
- Deepthi Ashokkumar
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
| | - Qinyu Zhang
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
| | - Christian Much
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
| | - Anita S Bledau
- Stem Cell Engineering, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
| | - Ronald Naumann
- Transgenic Core Facility, Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Dimitra Alexopoulou
- DRESDEN-concept Genome Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Fetscherstr. 105, 01307 Dresden, Germany
| | - Andreas Dahl
- DRESDEN-concept Genome Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Fetscherstr. 105, 01307 Dresden, Germany
| | - Neha Goveas
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
| | - Jun Fu
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
| | - Konstantinos Anastassiadis
- Stem Cell Engineering, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
| | - A Francis Stewart
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany
| | - Andrea Kranz
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, Tatzberg 47, 01307 Dresden, Germany
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19
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Spectrum-Wide Exploration of Human Adenoviruses for Breast Cancer Therapy. Cancers (Basel) 2020; 12:cancers12061403. [PMID: 32486014 PMCID: PMC7352696 DOI: 10.3390/cancers12061403] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 05/22/2020] [Accepted: 05/25/2020] [Indexed: 12/24/2022] Open
Abstract
Oncolytic adenoviruses (Ads) are promising tools for cancer therapeutics. However, most Ad-based therapies utilize Ad type 5 (Ad5), which displays unsatisfying efficiency in clinical trials, partly due to the low expression levels of its primary coxsackievirus and adenovirus receptor (CAR) on tumor cells. Since the efficacy of virotherapy strongly relies on efficient transduction of targeted tumor cells, initial screening of a broad range of viral agents to identify the most effective vehicles is essential. Using a novel Ad library consisting of numerous human Ads representing known Ad species, we evaluated the transduction efficiencies in four breast cancer (BC) cell lines. For each cell line over 20 Ad types were screened in a high-throughput manner based on reporter assays. Ad types featuring high transduction efficiencies were further investigated with respect to the percentage of transgene-positive cells and efficiencies of cellular entry in individual cell lines. Additionally, oncolytic assay was performed to test tumor cell lysis efficacy of selected Ad types. We found that all analyzed BC cell lines show low expression levels of CAR, while alternative receptors such as CD46, DSG-2, and integrins were also detected. We identified Ad3, Ad35, Ad37, and Ad52 as potential candidates for BC virotherapy.
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Expanding the Spectrum of Adenoviral Vectors for Cancer Therapy. Cancers (Basel) 2020; 12:cancers12051139. [PMID: 32370135 PMCID: PMC7281331 DOI: 10.3390/cancers12051139] [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: 04/03/2020] [Revised: 04/28/2020] [Accepted: 04/30/2020] [Indexed: 12/15/2022] Open
Abstract
Adenoviral vectors (AdVs) have attracted much attention in the fields of vaccine development and treatment for diseases such as genetic disorders and cancer. In this review, we discuss the utility of AdVs in cancer therapies. In recent years, AdVs were modified as oncolytic AdVs (OAs) that possess the characteristics of cancer cell-specific replication and killing. Different carriers such as diverse cells and extracellular vesicles are being explored for delivering OAs into cancer sites after systemic administration. In addition, there are also various strategies to improve cancer-specific replication of OAs, mainly through modifying the early region 1 (E1) of the virus genome. It has been documented that oncolytic viruses (OVs) function through stimulating the immune system, resulting in the inhibition of cancer progression and, in combination with classical immune modulators, the anti-cancer effect of OAs can be even further enforced. To enhance the cancer treatment efficacy, OAs are also combined with other standard treatments, including surgery, chemotherapy and radiotherapy. Adenovirus type 5 (Ad5) has mainly been explored to develop vectors for cancer treatment with different modulations. Only a limited number of the more than 100 identified AdV types were converted into OAs and, therefore, the construction of an adenovirus library for the screening of potential novel OA candidates is essential. Here, we provide a state-of-the-art overview of currently performed and completed clinic trials with OAs and an adenovirus library, providing novel possibilities for developing innovative adenoviral vectors for cancer treatment.
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21
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Lanigan TM, Kopera HC, Saunders TL. Principles of Genetic Engineering. Genes (Basel) 2020; 11:E291. [PMID: 32164255 PMCID: PMC7140808 DOI: 10.3390/genes11030291] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/28/2020] [Accepted: 03/06/2020] [Indexed: 12/12/2022] Open
Abstract
Genetic engineering is the use of molecular biology technology to modify DNA sequence(s) in genomes, using a variety of approaches. For example, homologous recombination can be used to target specific sequences in mouse embryonic stem (ES) cell genomes or other cultured cells, but it is cumbersome, poorly efficient, and relies on drug positive/negative selection in cell culture for success. Other routinely applied methods include random integration of DNA after direct transfection (microinjection), transposon-mediated DNA insertion, or DNA insertion mediated by viral vectors for the production of transgenic mice and rats. Random integration of DNA occurs more frequently than homologous recombination, but has numerous drawbacks, despite its efficiency. The most elegant and effective method is technology based on guided endonucleases, because these can target specific DNA sequences. Since the advent of clustered regularly interspaced short palindromic repeats or CRISPR/Cas9 technology, endonuclease-mediated gene targeting has become the most widely applied method to engineer genomes, supplanting the use of zinc finger nucleases, transcription activator-like effector nucleases, and meganucleases. Future improvements in CRISPR/Cas9 gene editing may be achieved by increasing the efficiency of homology-directed repair. Here, we describe principles of genetic engineering and detail: (1) how common elements of current technologies include the need for a chromosome break to occur, (2) the use of specific and sensitive genotyping assays to detect altered genomes, and (3) delivery modalities that impact characterization of gene modifications. In summary, while some principles of genetic engineering remain steadfast, others change as technologies are ever-evolving and continue to revolutionize research in many fields.
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Affiliation(s)
- Thomas M. Lanigan
- Biomedical Research Core Facilities, Vector Core, University of Michigan, Ann Arbor, MI 48109, USA; (T.M.L.); (H.C.K.)
- Department of Internal Medicine, Division of Rheumatology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Huira C. Kopera
- Biomedical Research Core Facilities, Vector Core, University of Michigan, Ann Arbor, MI 48109, USA; (T.M.L.); (H.C.K.)
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Thomas L. Saunders
- Biomedical Research Core Facilities, Transgenic Animal Model Core, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Internal Medicine, Division of Genetic Medicine, University of Michigan, Ann Arbor, MI 48109, USA
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22
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Zelensky AN, Schoonakker M, Brandsma I, Tijsterman M, van Gent DC, Essers J, Kanaar R. Low dose ionizing radiation strongly stimulates insertional mutagenesis in a γH2AX dependent manner. PLoS Genet 2020; 16:e1008550. [PMID: 31945059 PMCID: PMC6964834 DOI: 10.1371/journal.pgen.1008550] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 12/02/2019] [Indexed: 11/21/2022] Open
Abstract
Extrachromosomal DNA can integrate into the genome with no sequence specificity producing an insertional mutation. This process, which is referred to as random integration (RI), requires a double stranded break (DSB) in the genome. Inducing DSBs by various means, including ionizing radiation, increases the frequency of integration. Here we report that non-lethal physiologically relevant doses of ionizing radiation (10-100 mGy), within the range produced by medical imaging equipment, stimulate RI of transfected and viral episomal DNA in human and mouse cells with an extremely high efficiency. Genetic analysis of the stimulated RI (S-RI) revealed that it is distinct from the background RI, requires histone H2AX S139 phosphorylation (γH2AX) and is not reduced by DNA polymerase θ (Polq) inactivation. S-RI efficiency was unaffected by the main DSB repair pathway (homologous recombination and non-homologous end joining) disruptions, but double deficiency in MDC1 and 53BP1 phenocopies γH2AX inactivation. The robust responsiveness of S-RI to physiological amounts of DSBs can be exploited for extremely sensitive, macroscopic and direct detection of DSB-induced mutations, and warrants further exploration in vivo to determine if the phenomenon has implications for radiation risk assessment.
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Affiliation(s)
- Alex N. Zelensky
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
- Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Mascha Schoonakker
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Inger Brandsma
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marcel Tijsterman
- Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Dik C. van Gent
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
- Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jeroen Essers
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Radiation Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Vascular Surgery, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
- Oncode Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
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23
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Gao J, Mese K, Bunz O, Ehrhardt A. State‐of‐the‐art human adenovirus vectorology for therapeutic approaches. FEBS Lett 2019; 593:3609-3622. [DOI: 10.1002/1873-3468.13691] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/16/2019] [Accepted: 11/18/2019] [Indexed: 12/11/2022]
Affiliation(s)
- Jian Gao
- Faculty of Health Centre for Biomedical Education and Research (ZBAF) School of Human Medicine Institute of Virology and Microbiology Witten/Herdecke University Germany
| | - Kemal Mese
- Faculty of Health Centre for Biomedical Education and Research (ZBAF) School of Human Medicine Institute of Virology and Microbiology Witten/Herdecke University Germany
| | - Oskar Bunz
- Faculty of Health Centre for Biomedical Education and Research (ZBAF) School of Human Medicine Institute of Virology and Microbiology Witten/Herdecke University Germany
| | - Anja Ehrhardt
- Faculty of Health Centre for Biomedical Education and Research (ZBAF) School of Human Medicine Institute of Virology and Microbiology Witten/Herdecke University Germany
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24
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Bereshchenko O, Lo Re O, Nikulenkov F, Flamini S, Kotaskova J, Mazza T, Le Pannérer MM, Buschbeck M, Giallongo C, Palumbo G, Li Volti G, Pazienza V, Cervinek L, Riccardi C, Krejci L, Pospisilova S, Stewart AF, Vinciguerra M. Deficiency and haploinsufficiency of histone macroH2A1.1 in mice recapitulate hematopoietic defects of human myelodysplastic syndrome. Clin Epigenetics 2019; 11:121. [PMID: 31439048 PMCID: PMC6704528 DOI: 10.1186/s13148-019-0724-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 08/12/2019] [Indexed: 12/19/2022] Open
Abstract
Background Epigenetic regulation is important in hematopoiesis, but the involvement of histone variants is poorly understood. Myelodysplastic syndromes (MDS) are heterogeneous clonal hematopoietic stem cell (HSC) disorders characterized by ineffective hematopoiesis. MacroH2A1.1 is a histone H2A variant that negatively correlates with the self-renewal capacity of embryonic, adult, and cancer stem cells. MacroH2A1.1 is a target of the frequent U2AF1 S34F mutation in MDS. The role of macroH2A1.1 in hematopoiesis is unclear. Results MacroH2A1.1 mRNA levels are significantly decreased in patients with low-risk MDS presenting with chromosomal 5q deletion and myeloid cytopenias and tend to be decreased in MDS patients carrying the U2AF1 S34F mutation. Using an innovative mouse allele lacking the macroH2A1.1 alternatively spliced exon, we investigated whether macroH2A1.1 regulates HSC homeostasis and differentiation. The lack of macroH2A1.1 decreased while macroH2A1.1 haploinsufficiency increased HSC frequency upon irradiation. Moreover, bone marrow transplantation experiments showed that both deficiency and haploinsufficiency of macroH2A1.1 resulted in enhanced HSC differentiation along the myeloid lineage. Finally, RNA-sequencing analysis implicated macroH2A1.1-mediated regulation of ribosomal gene expression in HSC homeostasis. Conclusions Together, our findings suggest a new epigenetic process contributing to hematopoiesis regulation. By combining clinical data with a discrete mutant mouse model and in vitro studies of human and mouse cells, we identify macroH2A1.1 as a key player in the cellular and molecular features of MDS. These data justify the exploration of macroH2A1.1 and associated proteins as therapeutic targets in hematological malignancies. Electronic supplementary material The online version of this article (10.1186/s13148-019-0724-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Oxana Bereshchenko
- Department of Medicine, Department of Philosophy, Social Sciences and Education, University of Perugia, Perugia, Italy.
| | - Oriana Lo Re
- International Clinical Research Center, St'Anne University Hospital, Brno, Czech Republic.,Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Fedor Nikulenkov
- International Clinical Research Center, St'Anne University Hospital, Brno, Czech Republic.,Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Sara Flamini
- Department of Medicine, Department of Philosophy, Social Sciences and Education, University of Perugia, Perugia, Italy
| | - Jana Kotaskova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine - Hematology and Oncology, Faculty of Medicine, University Hospital Brno and Masaryk University, Brno, Czech Republic
| | - Tommaso Mazza
- IRCCS Casa Sollievo della Sofferenza, Bioinformatics unit, San Giovanni Rotondo, Italy
| | - Marguerite-Marie Le Pannérer
- Josep Carreras Leukemia Research Institute (IJC), Universitat Autònoma de Barcelona, Campus ICO-Germans Trias I Pujol, Badalona, Spain.,Programme of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain
| | - Marcus Buschbeck
- Josep Carreras Leukemia Research Institute (IJC), Universitat Autònoma de Barcelona, Campus ICO-Germans Trias I Pujol, Badalona, Spain.,Programme of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain
| | - Cesarina Giallongo
- Division of Hematology, A.O.U. Policlinico-OVE, University of Catania, Catania, Italy
| | - Giuseppe Palumbo
- Department of Medical and Surgical Sciences and Advanced Technologies "GF Ingrassia", University of Catania, Catania, Italy
| | - Giovanni Li Volti
- Department of Biomedical and Biotechnological Sciences, University of Catania, Catania, Italy
| | - Valerio Pazienza
- Gastroenterology unit, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Libor Cervinek
- Department of Internal Medicine - Hematology and Oncology, Faculty of Medicine, University Hospital Brno and Masaryk University, Brno, Czech Republic
| | - Carlo Riccardi
- Department of Medicine, Department of Philosophy, Social Sciences and Education, University of Perugia, Perugia, Italy
| | - Lumir Krejci
- International Clinical Research Center, St'Anne University Hospital, Brno, Czech Republic.,Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Department of Internal Medicine - Hematology and Oncology, Faculty of Medicine, University Hospital Brno and Masaryk University, Brno, Czech Republic
| | - A Francis Stewart
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Manlio Vinciguerra
- International Clinical Research Center, St'Anne University Hospital, Brno, Czech Republic.
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Wang H, Li Z, Jia R, Yin J, Li A, Xia L, Yin Y, Müller R, Fu J, Stewart AF, Zhang Y. ExoCET: exonuclease in vitro assembly combined with RecET recombination for highly efficient direct DNA cloning from complex genomes. Nucleic Acids Res 2019; 46:e28. [PMID: 29240926 PMCID: PMC5861427 DOI: 10.1093/nar/gkx1249] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 12/02/2017] [Indexed: 12/29/2022] Open
Abstract
The exponentially increasing volumes of DNA sequence data highlight the need for new DNA cloning methods to explore the new information. Here, we describe ‘ExoCET’ (Exonuclease Combined with RecET recombination) to directly clone any chosen region from bacterial and mammalian genomes with nucleotide precision into operational plasmids. ExoCET combines in vitro exonuclease and annealing with the remarkable capacity of full length RecET homologous recombination (HR) to retrieve specified regions from genomic DNA preparations. Using T4 polymerase (T4pol) as the in vitro exonuclease for ExoCET, we directly cloned large regions (>50 kb) from bacterial and mammalian genomes, including DNA isolated from blood. Employing RecET HR or Cas9 cleavage in vitro, the directly cloned region can be chosen with nucleotide precision to position, for example, a gene into an expression vector without the need for further subcloning. In addition to its utility for bioprospecting in bacterial genomes, ExoCET presents straightforward access to mammalian genomes for various applications such as region-specific DNA sequencing that retains haplotype phasing, the rapid construction of optimal, haplotypic, isogenic targeting constructs or a new way to genotype that presents advantages over Southern blotting or polymerase chain reaction. The direct cloning capacities of ExoCET present new freedoms in recombinant DNA technology.
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Affiliation(s)
- Hailong Wang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
| | - Zhen Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
| | - Ruonan Jia
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
| | - Jia Yin
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
| | - Aiying Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
| | - Liqiu Xia
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, 410081 Changsha, People's Republic of China
| | - Yulong Yin
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China.,State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, 410081 Changsha, People's Republic of China.,Key Laboratory of Subtropical Agro-ecology, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, Hunan Province 410125, People's Republic of China
| | - Rolf Müller
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China.,Department of Microbial Natural Products, Helmholtz-Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI) and Pharmaceutical Biotechnology, Saarland University, Campus C2 3, 66123 Saarbrücken, Germany
| | - Jun Fu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
| | - A Francis Stewart
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Tatzberg 47-51, 01307 Dresden, Germany
| | - Youming Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
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26
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Proteomic navigation using proximity-labeling. Methods 2019; 164-165:67-72. [PMID: 30953756 DOI: 10.1016/j.ymeth.2019.03.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 10/27/2022] Open
Abstract
The identification of bona fide protein-protein interactions and the mapping of proteomes was greatly enhanced by protein tagging for generic affinity purification methods and analysis by mass spectrometry (AP-MS). The high quality of AP-MS data permitted the development of proteomic navigation by sequential tagging of identified interactions. However AP-MS is laborious and limited to relatively high affinity protein-protein interactions. Proximity labeling, first with the biotin ligase BirA, termed BioID, and then with ascorbate peroxidase, termed APEX, permits a greater reach into the proteome than AP-MS enabling both the identification of a wider field and weaker protein-protein interactions. This additional reach comes with the need for stringent controls. Proximity labeling also permits experiments in living cells allowing spatiotemporal investigations of the proteome. Here we discuss proximity labeling with accompanying methodological descriptions for E. coli and mammalian cells.
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27
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Caldwell BJ, Bell CE. Structure and mechanism of the Red recombination system of bacteriophage λ. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 147:33-46. [PMID: 30904699 DOI: 10.1016/j.pbiomolbio.2019.03.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/05/2019] [Accepted: 03/15/2019] [Indexed: 01/27/2023]
Abstract
While much of this volume focuses on mammalian DNA repair systems that are directly involved in genome stability and cancer, it is important to still be mindful of model systems from prokaryotes. Herein we review the Red recombination system of bacteriophage λ, which consists of an exonuclease for resecting dsDNA ends, and a single-strand annealing protein (SSAP) for binding the resulting 3'-overhang and annealing it to a complementary strand. The genetics and biochemistry of Red have been studied for over 50 years, in work that has laid much of the foundation for understanding DNA recombination in higher eukaryotes. In fact, the Red exonuclease (λ exo) is homologous to Dna2, a nuclease involved in DNA end-resection in eukaryotes, and the Red annealing protein (Redβ) is homologous to Rad52, the primary SSAP in eukaryotes. While eukaryotic recombination involves an elaborate network of proteins that is still being unraveled, the phage systems are comparatively simple and streamlined, yet still encompass the fundamental features of recombination, namely DNA end-resection, homologous pairing (annealing), and a coupling between them. Moreover, the Red system has been exploited in powerful methods for bacterial genome engineering that are important for functional genomics and systems biology. However, several mechanistic aspects of Red, particularly the action of the annealing protein, remain poorly understood. This review will focus on the proteins of the Red recombination system, with particular attention to structural and mechanistic aspects, and how the lessons learned can be applied to eukaryotic systems.
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Affiliation(s)
- Brian J Caldwell
- Ohio State Biochemistry Program, The Ohio State University, 484 West 12th Avenue, Columbus, OH, 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, 1060 Carmack Road, Columbus, OH, 43210, USA
| | - Charles E Bell
- Ohio State Biochemistry Program, The Ohio State University, 484 West 12th Avenue, Columbus, OH, 43210, USA; Department of Biological Chemistry and Pharmacology, The Ohio State University, 1060 Carmack Road, Columbus, OH, 43210, USA; Department of Chemistry and Biochemistry, 484 West 12th Avenue, 1060 Carmack Road, Columbus, OH, 43210, USA.
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28
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Yin J, Zheng W, Gao Y, Jiang C, Shi H, Diao X, Li S, Chen H, Wang H, Li R, Li A, Xia L, Yin Y, Stewart AF, Zhang Y, Fu J. Single-Stranded DNA-Binding Protein and Exogenous RecBCD Inhibitors Enhance Phage-Derived Homologous Recombination in Pseudomonas. iScience 2019; 14:1-14. [PMID: 30921732 PMCID: PMC6438905 DOI: 10.1016/j.isci.2019.03.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 12/28/2018] [Accepted: 03/07/2019] [Indexed: 12/25/2022] Open
Abstract
The limited efficiency of the available tools for genetic manipulation of Pseudomonas limits fundamental research and utilization of this genus. We explored the properties of a lambda Red-like operon (BAS) from Pseudomonas aeruginosa phage Ab31 and a Rac bacteriophage RecET-like operon (RecTEPsy) from Pseudomonas syringae pv. syringae B728a. Compared with RecTEPsy, the BAS operon was functional at a higher temperature indicating potential to be a generic system for Pseudomonas. Owing to the lack of RecBCD inhibitor in the BAS operon, we added Redγ or Pluγ and found increased recombineering efficiencies in P. aeruginosa and Pseudomonas fluorescens but not in Pseudomonas putida and P. syringae. Overexpression of single-stranded DNA-binding protein enhanced recombineering in several contexts including RecET recombination in E. coli. The utility of these systems was demonstrated by engineering P. aeruginosa genomes to create an attenuated rhamnolipid producer. Our work enhances the potential for functional genomics in Pseudomonas. The BAS operon is a generic recombineering system for Pseudomonas species Single-stranded DNA-binding proteins (SSBs) can stimulate homologous recombination The heterologous gam genes can inhibit RecBCD function in Pseudomonas
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Affiliation(s)
- Jia Yin
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China; Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, 410081 Changsha, China
| | - Wentao Zheng
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China
| | - Yunsheng Gao
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China
| | - Chanjuan Jiang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China
| | - Hongbo Shi
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China
| | - Xiaotong Diao
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China
| | - Shanshan Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China
| | - Hanna Chen
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, 410081 Changsha, China
| | - Hailong Wang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China
| | - Ruijuan Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China
| | - Aiying Li
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China
| | - Liqiu Xia
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, 410081 Changsha, China
| | - Yulong Yin
- Hunan International Joint Laboratory of Animal Intestinal Ecology and Health, Laboratory of Animal Nutrition and Human Health, College of Life Sciences, Hunan Normal University, 410081 Changsha, China; Chinese Academy of Science, Institute of Subtropical Agriculture, Research Center for Healthy Breeding of Livestock and Poultry, Hunan Engineering and Research Center of Animal and Poultry Science and Key Laboratory for Agroecological Processes in Subtropical Region, Scientific Observation and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, 410125 Changsha, China
| | - A Francis Stewart
- Biotechnology Research Center, Center for Molecular and Cellular Bioengineering, Dresden University of Technology, BioInnovationsZentrum, Tatzberg 47-51, 01307 Dresden, Germany.
| | - Youming Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China.
| | - Jun Fu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Suzhou Institute of Shandong University, 266235 Qingdao, China.
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29
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Zhao J, Zong W, Zhao Y, Gou D, Liang S, Shen J, Wu Y, Zheng X, Wu R, Wang X, Niu F, Wang A, Zhang Y, Xiong JW, Chen L, Liu Y. In vivo imaging of β-cell function reveals glucose-mediated heterogeneity of β-cell functional development. eLife 2019; 8:41540. [PMID: 30694176 PMCID: PMC6395064 DOI: 10.7554/elife.41540] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 01/29/2019] [Indexed: 12/22/2022] Open
Abstract
How pancreatic β-cells acquire function in vivo is a long-standing mystery due to the lack of technology to visualize β-cell function in living animals. Here, we applied a high-resolution two-photon light-sheet microscope for the first in vivo imaging of Ca2+activity of every β-cell in Tg (ins:Rcamp1.07) zebrafish. We reveal that the heterogeneity of β-cell functional development in vivo occurred as two waves propagating from the islet mantle to the core, coordinated by islet vascularization. Increasing amounts of glucose induced functional acquisition and enhancement of β-cells via activating calcineurin/nuclear factor of activated T-cells (NFAT) signaling. Conserved in mammalians, calcineurin/NFAT prompted high-glucose-stimulated insulin secretion of neonatal mouse islets cultured in vitro. However, the reduction in low-glucose-stimulated insulin secretion was dependent on optimal glucose but independent of calcineurin/NFAT. Thus, combination of optimal glucose and calcineurin activation represents a previously unexplored strategy for promoting functional maturation of stem cell-derived β-like cells in vitro. When the amount of sugar in our body rises, specialised cells known as β-cells respond by releasing insulin, a hormone that acts on various organs to keep blood sugar levels within a healthy range. These cells cluster in small ‘islets’ inside our pancreas. If the number of working β-cells declines, diseases such as diabetes may appear and it becomes difficult to regulate the amount of sugar in our bodies. Understanding how β-cells normally develop and mature in the embryo could help us learn how to make new ones in the laboratory. In particular, researchers are interested in studying how different body signals, such as blood sugar levels, turn immature β-cells into fully productive cells. However, in mammals, the pancreas and its islets are buried deep inside the embryo and they cannot be observed easily. Here, Zhao et al. circumvented this problem by doing experiments on zebrafish embryos, which are transparent, grow outside their mother’s body, and have pancreatic islets that are similar to the ones found in mammals. A three-dimensional microscopy technique was used to watch individual β-cells activity over long periods, which revealed that the cells start being able to produce insulin at different times. The β-cells around the edge of each islet were the first to have access to blood sugar signals: they gained their hormone-producing role earlier than the cells in the core of an islet, which only sensed the information later on. Zhao et al. then exposed the zebrafish embryos to different amounts of sugar. This showed that there is an optimal concentration of sugar which helps β-cells develop by kick-starting a cascade of events inside the cell. Further experiments confirmed that the same pathway and optimal sugar concentration exist for mammalian islets grown in the laboratory. These findings may help researchers find better ways of making new β-cells to treat diabetic patients. In the future, using the three-dimensional imaging technique in zebrafish embryos may lead to more discoveries on how the pancreas matures.
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Affiliation(s)
- Jia Zhao
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Weijian Zong
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,China Department of Cognitive Sciences, Institute of Basic Medical Sciences, Beijing, China
| | - Yiwen Zhao
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Dongzhou Gou
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Shenghui Liang
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Jiayu Shen
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Yi Wu
- School of Software and Microelectronics, Peking University, Beijing, China
| | - Xuan Zheng
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Runlong Wu
- School of Electronics Engineering and Computer Science, Peking University, Beijing, China
| | - Xu Wang
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Fuzeng Niu
- State Key Laboratory of Advanced Optical Communication System and Networks, School of Electronics Engineering and Computer Science, Peking University, Beijing, China
| | - Aimin Wang
- State Key Laboratory of Advanced Optical Communication System and Networks, School of Electronics Engineering and Computer Science, Peking University, Beijing, China
| | - Yunfeng Zhang
- School of Electronics Engineering and Computer Science, Peking University, Beijing, China
| | - Jing-Wei Xiong
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Liangyi Chen
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China
| | - Yanmei Liu
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing, China.,Institute for Brain Research and Rehabilitation (IBRR), Guangdong Key Laboratory of Mental Health and Cognitive Science, South China Normal University, Guangzhou, China
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30
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Yu F, Jing X, Li X, Wang H, Chen H, Zhong L, Yin J, Pan D, Yin Y, Fu J, Xia L, Bian X, Tu Q, Zhang Y. Recombineering Pseudomonas protegens CHA0: An innovative approach that improves nitrogen fixation with impressive bactericidal potency. Microbiol Res 2019; 218:58-65. [DOI: 10.1016/j.micres.2018.09.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 08/06/2018] [Accepted: 09/28/2018] [Indexed: 10/28/2022]
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31
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Percin GI, Eitler J, Kranz A, Fu J, Pollard JW, Naumann R, Waskow C. CSF1R regulates the dendritic cell pool size in adult mice via embryo-derived tissue-resident macrophages. Nat Commun 2018; 9:5279. [PMID: 30538245 PMCID: PMC6290072 DOI: 10.1038/s41467-018-07685-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 05/05/2018] [Indexed: 12/14/2022] Open
Abstract
Regulatory mechanisms controlling the pool size of spleen dendritic cells (DC) remain incompletely understood. DCs are continuously replenished from hematopoietic stem cells, and FLT3-mediated signals cell-intrinsically regulate homeostatic expansion of spleen DCs. Here we show that combining FLT3 and CSF1R-deficiencies results in specific and complete abrogation of spleen DCs in vivo. Spatiotemporally controlled CSF1R depletion reveals a cell-extrinsic and non-hematopoietic mechanism for DC pool size regulation. Lack of CSF1R-mediated signals impedes the differentiation of spleen macrophages of embryonic origin, and the resulted macrophage depletion during development or in adult mice results in loss of DCs. Moreover, embryo-derived macrophages are important for the physiologic regeneration of DC after activation-induced depletion in situ. In summary, we show that the differentiation of DC and their regeneration relies on ontogenetically distinct spleen macrophages, thereby providing a novel regulatory principle that may also be important for the differentiation of other hematopoietic cell types.
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Affiliation(s)
- Gulce Itir Percin
- Regeneration in Hematopoiesis and Animal Models in Hematopoiesis, Institute for Immunology, Fetscherstr. 74, 01307, Dresden, Germany
- Regeneration in Hematopoiesis, Leibniz-Institute on Aging - Fritz-Lipmann-Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany
| | - Jiri Eitler
- Regeneration in Hematopoiesis and Animal Models in Hematopoiesis, Institute for Immunology, Fetscherstr. 74, 01307, Dresden, Germany
| | - Andrea Kranz
- Genomics, Biotechnology Center, TU Dresden, BioInnovationsZentrum, Tatzberg 47-49, 01307, Dresden, Germany
| | - Jun Fu
- Genomics, Biotechnology Center, TU Dresden, BioInnovationsZentrum, Tatzberg 47-49, 01307, Dresden, Germany
| | - Jeffrey W Pollard
- MRC and University of Edinburgh Centre for Reproductive Health, Queen's Medical Research Institute, 47 Little France Crescent, Edinburgh, EH16 4TJ, UK
- Edinburgh Cancer Research UK Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Crewe Road S, Edinburgh, EH16 4TJ, Scotland, UK
| | - Ronald Naumann
- Max Planck Institute of Molecular Cell Biology and Genetics, Transgenic Core Facility, Pfotenhauerstr. 108, 01307, Dresden, Germany
| | - Claudia Waskow
- Regeneration in Hematopoiesis and Animal Models in Hematopoiesis, Institute for Immunology, Fetscherstr. 74, 01307, Dresden, Germany.
- Regeneration in Hematopoiesis, Leibniz-Institute on Aging - Fritz-Lipmann-Institute (FLI), Beutenbergstrasse 11, 07745, Jena, Germany.
- Department of Medicine III, Faculty of Medicine, TU Dresden, Fetscherstrasse 74, 01307, Dresden, Germany.
- Faculty of Biological Sciences, Friedrich-Schiller University, Fürstengraben 1, 07743, Jena, Germany.
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32
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A single reporter mouse line for Vika, Flp, Dre, and Cre-recombination. Sci Rep 2018; 8:14453. [PMID: 30262904 PMCID: PMC6160450 DOI: 10.1038/s41598-018-32802-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 09/13/2018] [Indexed: 11/28/2022] Open
Abstract
Site-specific recombinases (SSR) are utilized as important genome engineering tools to precisely modify the genome of mice and other model organisms. Reporter mice that mark cells that at any given time had expressed the enzyme are frequently used for lineage tracing and to characterize newly generated mice expressing a recombinase from a chosen promoter. With increasing sophistication of genome alteration strategies, the demand for novel SSR systems that efficiently and specifically recombine their targets is rising and several SSR-systems are now used in combination to address complex biological questions in vivo. Generation of reporter mice for each one of these recombinases is cumbersome and increases the number of mouse lines that need to be maintained in animal facilities. Here we present a multi-reporter mouse line for loci-of-recombination (X) (MuX) that streamlines the characterization of mice expressing prominent recombinases. MuX mice constitutively express nuclear green fluorescent protein after recombination by either Cre, Flp, Dre or Vika recombinase, rationalizing the number of animal lines that need to be maintained. We also pioneer the use of the Vika/vox system in mice, illustrating its high efficacy and specificity, thereby facilitating future designs of sophisticated recombinase-based in vivo genome engineering strategies.
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33
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Zhang W, Fu J, Ehrhardt A. Novel Vector Construction Based on Alternative Adenovirus Types via Homologous Recombination. Hum Gene Ther Methods 2018; 29:124-134. [PMID: 29756505 DOI: 10.1089/hgtb.2018.044] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Adenoviral vector (AdV) is one of the most used vectors in gene therapy clinical trials. However the therapeutic effect of AdV is limited due to preexisting immunity to the currently used human adenovirus type 5 and pre-decided vector tropism. It is highly demanded to develop novel AdVs originated from other types than adenovirus type 5. Here, we describe a method for direct cloning of adenovirus utilizing linear-linear homologous recombination, followed by rapid adenoviral genome modification via linear-circular homologous recombination. A plasmid bearing chosen adenoviral genome with the desired modification is generated in three weeks, from which a novel AdV can be reconstituted.
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Affiliation(s)
- Wenli Zhang
- 1 Chair for Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University , Witten, Germany
| | - Jun Fu
- 2 Shandong University-Helmholtz Joint Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University , Qingdao, China
| | - Anja Ehrhardt
- 1 Chair for Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University , Witten, Germany
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34
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Zhang W, Fu J, Liu J, Wang H, Schiwon M, Janz S, Schaffarczyk L, von der Goltz L, Ehrke-Schulz E, Dörner J, Solanki M, Boehme P, Bergmann T, Lieber A, Lauber C, Dahl A, Petzold A, Zhang Y, Stewart AF, Ehrhardt A. An Engineered Virus Library as a Resource for the Spectrum-wide Exploration of Virus and Vector Diversity. Cell Rep 2018; 19:1698-1709. [PMID: 28538186 DOI: 10.1016/j.celrep.2017.05.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 04/12/2017] [Accepted: 05/02/2017] [Indexed: 12/18/2022] Open
Abstract
Adenoviruses (Ads) are large human-pathogenic double-stranded DNA (dsDNA) viruses presenting an enormous natural diversity associated with a broad variety of diseases. However, only a small fraction of adenoviruses has been explored in basic virology and biomedical research, highlighting the need to develop robust and adaptable methodologies and resources. We developed a method for high-throughput direct cloning and engineering of adenoviral genomes from different sources utilizing advanced linear-linear homologous recombination (LLHR) and linear-circular homologous recombination (LCHR). We describe 34 cloned adenoviral genomes originating from clinical samples, which were characterized by next-generation sequencing (NGS). We anticipate that this recombineering strategy and the engineered adenovirus library will provide an approach to study basic and clinical virology. High-throughput screening (HTS) of the reporter-tagged Ad library in a panel of cell lines including osteosarcoma disease-specific cell lines revealed alternative virus types with enhanced transduction and oncolysis efficiencies. This highlights the usefulness of this resource.
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Affiliation(s)
- Wenli Zhang
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Jun Fu
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, People's Republic of China; Genomics, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Jing Liu
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Hailong Wang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, People's Republic of China; Genomics, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Maren Schiwon
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Sebastian Janz
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Lukas Schaffarczyk
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Lukas von der Goltz
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Eric Ehrke-Schulz
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Johannes Dörner
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Manish Solanki
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Philip Boehme
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Thorsten Bergmann
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany
| | - Andre Lieber
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195-7720, USA
| | - Chris Lauber
- Institute for Medical Informatics and Biometry, Carl Gustav Carus, Faculty of Medicine, Technische Universität Dresden, 01307 Dresden, Germany
| | - Andreas Dahl
- Deep Sequencing, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Andreas Petzold
- Deep Sequencing, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany
| | - Youming Zhang
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Jinan 250100, People's Republic of China.
| | - A Francis Stewart
- Genomics, Biotechnology Center, Technische Universität Dresden, 01307 Dresden, Germany.
| | - Anja Ehrhardt
- Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Department of Human Medicine, Faculty of Health, Witten/Herdecke University, 58453 Witten, Germany.
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35
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Zhang W, Ehrhardt A. Getting genetic access to natural adenovirus genomes to explore vector diversity. Virus Genes 2017; 53:675-683. [PMID: 28711987 DOI: 10.1007/s11262-017-1487-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 07/06/2017] [Indexed: 01/20/2023]
Abstract
Recombinant vectors based on the human adenovirus type 5 (HAdV5) have been developed and extensively used in preclinical and clinical studies for over 30 years. However, certain restrictions of HAdV5-based vectors have limited their clinical applications because they are rather inefficient in specifically transducing cells of therapeutic interest that lack the coxsackievirus and adenovirus receptor (CAR). Moreover, enhanced vector-associated toxicity and widespread preexisting immunity have been shown to significantly hamper the effectiveness of HAdV-5-mediated gene transfer. However, evolution of adenoviruses in the natural host is driving the generation of novel types with altered virulence, enhanced transmission, and altered tissue tropism. As a consequence, an increasing number of alternative adenovirus types were identified, which may represent a valuable resource for the development of novel vector types. Thus, researchers are focusing on the other naturally occurring adenovirus types, which are structurally similar but functionally different from HAdV5. To this end, several strategies have been devised for getting genetic access to adenovirus genomes, resulting in a new panel of adenoviral vectors. Importantly, these vectors were shown to have a host range different from HAdV5 and to escape the anti-HAdV5 immune response, thus underlining the great potential of this approach. In summary, this review provides a state-of-the-art overview of one essential step in adenoviral vector development.
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Affiliation(s)
- Wenli Zhang
- Department of Human Medicine, Faculty of Health, Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, 58453, Witten, Germany
| | - Anja Ehrhardt
- Department of Human Medicine, Faculty of Health, Institute of Virology and Microbiology, Center for Biomedical Education and Research (ZBAF), Witten/Herdecke University, 58453, Witten, Germany.
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36
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"Cre/loxP plus BAC": a strategy for direct cloning of large DNA fragment and its applications in Photorhabdus luminescens and Agrobacterium tumefaciens. Sci Rep 2016; 6:29087. [PMID: 27364376 PMCID: PMC4929569 DOI: 10.1038/srep29087] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 06/14/2016] [Indexed: 01/23/2023] Open
Abstract
Heterologous expression has been proven to be a valid strategy for elucidating the natural products produced by gene clusters uncovered by genome sequencing projects. Efforts have been made to efficiently clone gene clusters directly from genomic DNA and several approaches have been developed. Here, we present an alternative strategy based on the site-specific recombinase system Cre/loxP for direct cloning gene clusters. A type three secretion system (T3SS) gene cluster (~32 kb) from Photorhabdus luminescens TT01 and DNA fragment (~78 kb) containing the siderophore biosynthetic gene cluster from Agrobacterium tumefaciens C58 have been successfully cloned into pBeloBAC11 with “Cre/loxP plus BAC” strategy. Based on the fact that Cre/loxP system has successfully used for genomic engineering in a wide range of organisms, we believe that this strategy could be widely used for direct cloning of large DNA fragment.
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37
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Liao BK, Jörg DJ, Oates AC. Faster embryonic segmentation through elevated Delta-Notch signalling. Nat Commun 2016; 7:11861. [PMID: 27302627 PMCID: PMC4912627 DOI: 10.1038/ncomms11861] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 05/06/2016] [Indexed: 12/21/2022] Open
Abstract
An important step in understanding biological rhythms is the control of period. A multicellular, rhythmic patterning system termed the segmentation clock is thought to govern the sequential production of the vertebrate embryo's body segments, the somites. Several genetic loss-of-function conditions, including the Delta-Notch intercellular signalling mutants, result in slower segmentation. Here, we generate DeltaD transgenic zebrafish lines with a range of copy numbers and correspondingly increased signalling levels, and observe faster segmentation. The highest-expressing line shows an altered oscillating gene expression wave pattern and shortened segmentation period, producing embryos with more, shorter body segments. Our results reveal surprising differences in how Notch signalling strength is quantitatively interpreted in different organ systems, and suggest a role for intercellular communication in regulating the output period of the segmentation clock by altering its spatial pattern. Rhythmic patterning governs the formation of somites in vertebrates, but how the period of such rhythms can be changed is unclear. Here, the authors generate a genetic model in zebrafish to increase DeltaD expression, which increases the range of Delta-Notch signalling, causing faster segmentation.
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Affiliation(s)
- Bo-Kai Liao
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, Dresden 01037, Germany.,Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK
| | - David J Jörg
- Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, Dresden 01187, Germany
| | - Andrew C Oates
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, Dresden 01037, Germany.,Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, London NW7 1AA, UK.,Department of Cell and Developmental Biology, University College London, Gower Street, London WC1E 6BT, UK
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38
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Baker O, Gupta A, Obst M, Zhang Y, Anastassiadis K, Fu J, Stewart AF. RAC-tagging: Recombineering And Cas9-assisted targeting for protein tagging and conditional analyses. Sci Rep 2016; 6:25529. [PMID: 27216209 PMCID: PMC4877586 DOI: 10.1038/srep25529] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Accepted: 04/13/2016] [Indexed: 11/30/2022] Open
Abstract
A fluent method for gene targeting to establish protein tagged and ligand inducible conditional loss-of-function alleles is described. We couple new recombineering applications for one-step cloning of gRNA oligonucleotides and rapid generation of short-arm (~1 kb) targeting constructs with the power of Cas9-assisted targeting to establish protein tagged alleles in embryonic stem cells at high efficiency. RAC (Recombineering And Cas9)-tagging with Venus, BirM, APEX2 and the auxin degron is facilitated by a recombineering-ready plasmid series that permits the reuse of gene-specific reagents to insert different tags. Here we focus on protein tagging with the auxin degron because it is a ligand-regulated loss-of-function strategy that is rapid and reversible. Furthermore it includes the additional challenge of biallelic targeting. Despite high frequencies of monoallelic RAC-targeting, we found that simultaneous biallelic targeting benefits from long-arm (>4 kb) targeting constructs. Consequently an updated recombineering pipeline for fluent generation of long arm targeting constructs is also presented.
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Affiliation(s)
- Oliver Baker
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Ashish Gupta
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Mandy Obst
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Youming Zhang
- Shandong University–Helmholtz Joint Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Shanda Nanlu 27, 250100 Jinan, People’s Republic of China
| | - Konstantinos Anastassiadis
- Stem Cell Engineering, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
| | - Jun Fu
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
- Shandong University–Helmholtz Joint Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Shanda Nanlu 27, 250100 Jinan, People’s Republic of China
| | - A. Francis Stewart
- Genomics, Biotechnology Center, Technische Universität Dresden, BioInnovationsZentrum, Tatzberg 47, Dresden 01307, Germany
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39
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Meinke G, Bohm A, Hauber J, Pisabarro MT, Buchholz F. Cre Recombinase and Other Tyrosine Recombinases. Chem Rev 2016; 116:12785-12820. [PMID: 27163859 DOI: 10.1021/acs.chemrev.6b00077] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Tyrosine-type site-specific recombinases (T-SSRs) have opened new avenues for the predictable modification of genomes as they enable precise genome editing in heterologous hosts. These enzymes are ubiquitous in eubacteria, prevalent in archaea and temperate phages, present in certain yeast strains, but barely found in higher eukaryotes. As tools they find increasing use for the generation and systematic modification of genomes in a plethora of organisms. If applied in host organisms, they enable precise DNA cleavage and ligation without the gain or loss of nucleotides. Criteria directing the choice of the most appropriate T-SSR system for genetic engineering include that, whenever possible, the recombinase should act independent of cofactors and that the target sequences should be long enough to be unique in a given genome. This review is focused on recent advancements in our mechanistic understanding of simple T-SSRs and their application in developmental and synthetic biology, as well as in biomedical research.
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Affiliation(s)
- Gretchen Meinke
- Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine , Boston, Massachusetts 02111, United States
| | - Andrew Bohm
- Department of Developmental, Molecular & Chemical Biology, Tufts University School of Medicine , Boston, Massachusetts 02111, United States
| | - Joachim Hauber
- Heinrich Pette Institute, Leibniz Institute for Experimental Virology , 20251 Hamburg, Germany
| | | | - Frank Buchholz
- Medical Systems Biology, UCC, Medical Faculty Carl Gustav Carus TU Dresden , 01307 Dresden, Germany
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40
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Room temperature electrocompetent bacterial cells improve DNA transformation and recombineering efficiency. Sci Rep 2016; 6:24648. [PMID: 27095488 PMCID: PMC4837392 DOI: 10.1038/srep24648] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 04/04/2016] [Indexed: 01/20/2023] Open
Abstract
Bacterial competent cells are essential for cloning, construction of DNA libraries, and mutagenesis in every molecular biology laboratory. Among various transformation methods, electroporation is found to own the best transformation efficiency. Previous electroporation methods are based on washing and electroporating the bacterial cells in ice-cold condition that make them fragile and prone to death. Here we present simple temperature shift based methods that improve DNA transformation and recombineering efficiency in E. coli and several other gram-negative bacteria thereby economizing time and cost. Increased transformation efficiency of large DNA molecules is a significant advantage that might facilitate the cloning of large fragments from genomic DNA preparations and metagenomics samples.
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41
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Genetic engineering and heterologous expression of the disorazol biosynthetic gene cluster via Red/ET recombineering. Sci Rep 2016; 6:21066. [PMID: 26875499 PMCID: PMC4753468 DOI: 10.1038/srep21066] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 01/18/2016] [Indexed: 11/08/2022] Open
Abstract
Disorazol, a macrocyclic polykitide produced by the myxobacterium Sorangium cellulosum So ce12 and it is reported to have potential cytotoxic activity towards several cancer cell lines, including multi-drug resistant cells. The disorazol biosynthetic gene cluster (dis) from Sorangium cellulosum (So ce12) was identified by transposon mutagenesis and cloned in a bacterial artificial chromosome (BAC) library. The 58-kb dis core gene cluster was reconstituted from BACs via Red/ET recombineering and expressed in Myxococcus xanthus DK1622. For the first time ever, a myxobacterial trans-AT polyketide synthase has been expressed heterologously in this study. Expression in M. xanthus allowed us to optimize the yield of several biosynthetic products using promoter engineering. The insertion of an artificial synthetic promoter upstream of the disD gene encoding a discrete acyl transferase (AT), together with an oxidoreductase (Or), resulted in 7-fold increase in disorazol production. The successful reconstitution and expression of the genetic sequences encoding for these promising cytotoxic compounds will allow combinatorial biosynthesis to generate novel disorazol derivatives for further bioactivity evaluation.
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Wong FK, Fei JF, Mora-Bermúdez F, Taverna E, Haffner C, Fu J, Anastassiadis K, Stewart AF, Huttner WB. Sustained Pax6 Expression Generates Primate-like Basal Radial Glia in Developing Mouse Neocortex. PLoS Biol 2015; 13:e1002217. [PMID: 26252244 PMCID: PMC4529158 DOI: 10.1371/journal.pbio.1002217] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 06/30/2015] [Indexed: 11/21/2022] Open
Abstract
The evolutionary expansion of the neocortex in mammals has been linked to enlargement of the subventricular zone (SVZ) and increased proliferative capacity of basal progenitors (BPs), notably basal radial glia (bRG). The transcription factor Pax6 is known to be highly expressed in primate, but not mouse, BPs. Here, we demonstrate that sustaining Pax6 expression selectively in BP-genic apical radial glia (aRG) and their BP progeny of embryonic mouse neocortex suffices to induce primate-like progenitor behaviour. Specifically, we conditionally expressed Pax6 by in utero electroporation using a novel, Tis21–CreERT2 mouse line. This expression altered aRG cleavage plane orientation to promote bRG generation, increased cell-cycle re-entry of BPs, and ultimately increased upper-layer neuron production. Upper-layer neuron production was also increased in double-transgenic mouse embryos with sustained Pax6 expression in the neurogenic lineage. Strikingly, increased BPs existed not only in the SVZ but also in the intermediate zone of the neocortex of these double-transgenic mouse embryos. In mutant mouse embryos lacking functional Pax6, the proportion of bRG among BPs was reduced. Our data identify specific Pax6 effects in BPs and imply that sustaining this Pax6 function in BPs could be a key aspect of SVZ enlargement and, consequently, the evolutionary expansion of the neocortex. "Humanizing" the expression of the transcription factor Pax6 in cortical progenitors in the developing mouse brain is sufficient to endow these progenitors with a primate-like proliferative capacity. During development, neural progenitors generate all cells that make up the mammalian brain. Differences in brain size among the various mammalian species are attributed to differences in the abundance and proliferative capacity of a specific class of neural progenitors called basal progenitors. Among these, a specific progenitor type called basal radial glia is thought to have played an important role during evolution in the expansion of the neocortex, the part of the brain associated with higher cognitive functions like conscious thought and language. In the neocortex, the expression of the transcription factor Pax6 in basal progenitors is low in rodents, but high in primates, including humans. In this study, we aimed to mimic the elevated expression pattern of Pax6 seen in humans in basal progenitors of the embryonic mouse neocortex. To this end, we generated a novel, transgenic mouse line that allows sustained expression of the Pax6 gene in basal progenitors. This elevated expression resulted in an increase in the generation of basal radial glia, in the proliferative capacity of basal progenitors, and, ultimately, in the number of neurons produced. Our findings demonstrate that altering the expression of a single transcription factor from a mouse to a human-like pattern suffices to induce a primate-like proliferative behaviour in neural progenitors, which is thought to underlie the evolutionary expansion of the neocortex.
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Affiliation(s)
- Fong Kuan Wong
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Ji-Feng Fei
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | - Elena Taverna
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Christiane Haffner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Jun Fu
- Biotechnology Center of the Technische Universität Dresden, Dresden, Germany
| | | | - A. Francis Stewart
- Biotechnology Center of the Technische Universität Dresden, Dresden, Germany
| | - Wieland B. Huttner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- * E-mail:
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Ander M, Subramaniam S, Fahmy K, Stewart AF, Schäffer E. A Single-Strand Annealing Protein Clamps DNA to Detect and Secure Homology. PLoS Biol 2015; 13:e1002213. [PMID: 26271032 PMCID: PMC4535883 DOI: 10.1371/journal.pbio.1002213] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 06/26/2015] [Indexed: 11/24/2022] Open
Abstract
Repair of DNA breaks by single-strand annealing (SSA) is a major mechanism for the maintenance of genomic integrity. SSA is promoted by proteins (single-strand-annealing proteins [SSAPs]), such as eukaryotic RAD52 and λ phage Redβ. These proteins use a short single-stranded region to find sequence identity and initiate homologous recombination. However, it is unclear how SSAPs detect homology and catalyze annealing. Using single-molecule experiments, we provide evidence that homology is recognized by Redβ monomers that weakly hold single DNA strands together. Once annealing begins, dimerization of Redβ clamps the double-stranded region and nucleates nucleoprotein filament growth. In this manner, DNA clamping ensures and secures a successful detection for DNA sequence homology. The clamp is characterized by a structural change of Redβ and a remarkable stability against force up to 200 pN. Our findings not only present a detailed explanation for SSAP action but also identify the DNA clamp as a very stable, noncovalent, DNA-protein interaction.
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Affiliation(s)
- Marcel Ander
- Nanomechanics Group, Biotechnology Center, TU Dresden, Dresden, Germany
| | | | - Karim Fahmy
- Division of Biophysics, Institute of Resource Ecology, Helmholtz-Zentrum Dresden-Rossendorf, Dresden, Germany
| | - A. Francis Stewart
- Department of Genomics, Biotechnology Center, TU Dresden, Dresden, Germany
| | - Erik Schäffer
- Nanomechanics Group, Biotechnology Center, TU Dresden, Dresden, Germany
- Cellular Nanoscience, Center for Plant Molecular Biology (ZMBP), Universität Tübingen, Tübingen, Germany
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44
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Reddy TR, Kelsall EJ, Fevat LMS, Munson SE, Cowley SM. Differential requirements of singleplex and multiplex recombineering of large DNA constructs. PLoS One 2015; 10:e0125533. [PMID: 25954970 PMCID: PMC4425527 DOI: 10.1371/journal.pone.0125533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 03/16/2015] [Indexed: 11/18/2022] Open
Abstract
Recombineering is an in vivo genetic engineering technique involving homologous recombination mediated by phage recombination proteins. The use of recombineering methodology is not limited by size and sequence constraints and therefore has enabled the streamlined construction of bacterial strains and multi-component plasmids. Recombineering applications commonly utilize singleplex strategies and the parameters are extensively tested. However, singleplex recombineering is not suitable for the modification of several loci in genome recoding and strain engineering exercises, which requires a multiplex recombineering design. Defining the main parameters affecting multiplex efficiency especially the insertion of multiple large genes is necessary to enable efficient large-scale modification of the genome. Here, we have tested different recombineering operational parameters of the lambda phage Red recombination system and compared singleplex and multiplex recombineering of large gene sized DNA cassettes. We have found that optimal multiplex recombination required long homology lengths in excess of 120 bp. However, efficient multiplexing was possible with only 60 bp of homology. Multiplex recombination was more limited by lower amounts of DNA than singleplex recombineering and was greatly enhanced by use of phosphorothioate protection of DNA. Exploring the mechanism of multiplexing revealed that efficient recombination required co-selection of an antibiotic marker and the presence of all three Red proteins. Building on these results, we substantially increased multiplex efficiency using an ExoVII deletion strain. Our findings elucidate key differences between singleplex and multiplex recombineering and provide important clues for further improving multiplex recombination efficiency.
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Affiliation(s)
- Thimma R. Reddy
- Department of Biochemistry, University of Leicester, Leicester, LE1 9HN, United Kingdom
| | - Emma J. Kelsall
- Department of Biochemistry, University of Leicester, Leicester, LE1 9HN, United Kingdom
| | - Léna M. S. Fevat
- Center for Fisheries, Environment and Aquaculture Sciences, Lowestoft, NR33 0HT, United Kingdom
| | - Sarah E. Munson
- ES Cell Facility, Center for Core Biotechnology Services, Leicester, LE1 9HN, United Kingdom
| | - Shaun M. Cowley
- Department of Biochemistry, University of Leicester, Leicester, LE1 9HN, United Kingdom
- * E-mail:
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RNAi Interrogation of Dietary Modulation of Development, Metabolism, Behavior, and Aging in C. elegans. Cell Rep 2015; 11:1123-33. [PMID: 25959815 DOI: 10.1016/j.celrep.2015.04.024] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 01/29/2015] [Accepted: 04/11/2015] [Indexed: 02/06/2023] Open
Abstract
Diet affects nearly every aspect of animal life such as development, metabolism, behavior, and aging, both directly by supplying nutrients and indirectly through gut microbiota. C. elegans feeds on bacteria, and like other animals, different bacterial diets induce distinct dietary responses in the worm. However, the lack of certain critical tools hampers the use of worms as a model for dietary signaling. Here, we genetically engineered the bacterial strain OP50, the standard laboratory diet for C. elegans, making it compatible for dsRNA production and delivery. Using this RNAi-compatible OP50 strain and the other bacterial strain HT115, we feed worms different diets while delivering RNAi to interrogate the genetic basis underlying diet-dependent differential modulation of development, metabolism, behavior, and aging. We show by RNAi that neuroendocrine and mTOR pathways are involved in mediating differential dietary responses. This genetic tool greatly facilitates the use of C. elegans as a model for dietary signaling.
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46
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Reddy TR, Fevat LMS, Munson SE, Stewart AF, Cowley SM. Lambda red mediated gap repair utilizes a novel replicative intermediate in Escherichia coli. PLoS One 2015; 10:e0120681. [PMID: 25803509 PMCID: PMC4372340 DOI: 10.1371/journal.pone.0120681] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 02/05/2015] [Indexed: 11/19/2022] Open
Abstract
The lambda phage Red recombination system can mediate efficient homologous recombination in Escherichia coli, which is the basis of the DNA engineering technique termed recombineering. Red mediated insertion of DNA requires DNA replication, involves a single-stranded DNA intermediate and is more efficient on the lagging strand of the replication fork. Lagging strand recombination has also been postulated to explain the Red mediated repair of gapped plasmids by an Okazaki fragment gap filling model. Here, we demonstrate that gap repair involves a different strand independent mechanism. Gap repair assays examining the strand asymmetry of recombination did not show a lagging strand bias. Directly testing an ssDNA plasmid showed lagging strand recombination is possible but dsDNA plasmids did not employ this mechanism. Insertional recombination combined with gap repair also did not demonstrate preferential lagging strand bias, supporting a different gap repair mechanism. The predominant recombination route involved concerted insertion and subcloning though other routes also operated at lower frequencies. Simultaneous insertion of DNA resulted in modification of both strands and was unaffected by mutations to DNA polymerase I, responsible for Okazaki fragment maturation. The lower efficiency of an alternate Red mediated ends-in recombination pathway and the apparent lack of a Holliday junction intermediate suggested that gap repair does not involve a different Red recombination pathway. Our results may be explained by a novel replicative intermediate in gap repair that does not involve a replication fork. We exploited these observations by developing a new recombineering application based on concerted insertion and gap repair, termed SPI (subcloning plus insertion). SPI selected against empty vector background and selected for correct gap repair recombinants. We used SPI to simultaneously insert up to four different gene cassettes in a single recombineering reaction. Consequently, our findings have important implications for the understanding of E. coli replication and Red recombination.
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Affiliation(s)
- Thimma R. Reddy
- Department of Biochemistry, University of Leicester, Leicester, United Kingdom
| | - Léna M. S. Fevat
- Center for Fisheries, Environment and Aquaculture Sciences, Lowestoft, United Kingdom
| | - Sarah E. Munson
- ES Cell Facility, Centre for Core Biotechnology Services, University of Leicester, Leicester, United Kingdom
| | - A. Francis Stewart
- Genomics, BioInnovationsZentrum, Technische Universitaet Dresden, Dresden, Germany
| | - Shaun M. Cowley
- Department of Biochemistry, University of Leicester, Leicester, United Kingdom
- * E-mail:
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Bian X, Plaza A, Yan F, Zhang Y, Müller R. Rational and efficient site-directed mutagenesis of adenylation domain alters relative yields of luminmide derivatives in vivo. Biotechnol Bioeng 2015; 112:1343-53. [DOI: 10.1002/bit.25560] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 02/05/2015] [Indexed: 12/31/2022]
Affiliation(s)
- Xiaoying Bian
- Department of Microbial Natural Products; Helmholtz-Institute for Pharmaceutical Research Saarland; Helmholtz Centre for Infection Research; Campus C2 3, 66123 Saarbrücken Germany
- Department of Pharmaceutical Biotechnology; Saarland University; Campus C2 3, 66123 Saarbrücken Germany
- Shandong University-Helmholtz Institute of Biotechnology; State Key Laboratory of Microbial Technology; School of Life Science; Shandong University; Zhuzhou Road 168, 266101 Qingdao P. R. China
| | - Alberto Plaza
- Department of Microbial Natural Products; Helmholtz-Institute for Pharmaceutical Research Saarland; Helmholtz Centre for Infection Research; Campus C2 3, 66123 Saarbrücken Germany
- Department of Pharmaceutical Biotechnology; Saarland University; Campus C2 3, 66123 Saarbrücken Germany
| | - Fu Yan
- Department of Microbial Natural Products; Helmholtz-Institute for Pharmaceutical Research Saarland; Helmholtz Centre for Infection Research; Campus C2 3, 66123 Saarbrücken Germany
- Department of Pharmaceutical Biotechnology; Saarland University; Campus C2 3, 66123 Saarbrücken Germany
| | - Youming Zhang
- Shandong University-Helmholtz Institute of Biotechnology; State Key Laboratory of Microbial Technology; School of Life Science; Shandong University; Zhuzhou Road 168, 266101 Qingdao P. R. China
| | - Rolf Müller
- Department of Microbial Natural Products; Helmholtz-Institute for Pharmaceutical Research Saarland; Helmholtz Centre for Infection Research; Campus C2 3, 66123 Saarbrücken Germany
- Department of Pharmaceutical Biotechnology; Saarland University; Campus C2 3, 66123 Saarbrücken Germany
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48
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Reddy TR, Kelsall EJ, Fevat LMS, Munson SE, Cowley SM. Subcloning plus insertion (SPI)--a novel recombineering method for the rapid construction of gene targeting vectors. J Vis Exp 2015:e52155. [PMID: 25590226 PMCID: PMC4354499 DOI: 10.3791/52155] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Gene targeting refers to the precise modification of a genetic locus using homologous recombination. The generation of novel cell lines and transgenic mouse models using this method necessitates the construction of a ‘targeting’ vector, which contains homologous DNA sequences to the target gene, and has for many years been a limiting step in the process. Vector construction can be performed in vivo in Escherichia coli cells using homologous recombination mediated by phage recombinases using a technique termed recombineering. Recombineering is the preferred technique to subclone the long homology sequences (>4kb) and various targeting elements including selection markers that are required to mediate efficient allelic exchange between a targeting vector and its cognate genomic locus. Typical recombineering protocols follow an iterative scheme of step-wise integration of the targeting elements and require intermediate purification and transformation steps. Here, we present a novel recombineering methodology of vector assembly using a multiplex approach. Plasmid gap repair is performed by the simultaneous capture of genomic sequence from mouse Bacterial Artificial Chromosome libraries and the insertion of dual bacterial and mammalian selection markers. This subcloning plus insertion method is highly efficient and yields a majority of correct recombinants. We present data for the construction of different types of conditional gene knockout, or knock-in, vectors and BAC reporter vectors that have been constructed using this method. SPI vector construction greatly extends the repertoire of the recombineering toolbox and provides a simple, rapid and cost-effective method of constructing these highly complex vectors.
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Affiliation(s)
| | | | - Léna M S Fevat
- Center for Fisheries, Environment and Aquaculture Sciences
| | - Sarah E Munson
- ES Cell Facility, Centre for Core Biotechnology Services, University of Leicester
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Yin J, Zhu H, Xia L, Ding X, Hoffmann T, Hoffmann M, Bian X, Müller R, Fu J, Stewart AF, Zhang Y. A new recombineering system for Photorhabdus and Xenorhabdus. Nucleic Acids Res 2014; 43:e36. [PMID: 25539914 PMCID: PMC4381043 DOI: 10.1093/nar/gku1336] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 12/10/2014] [Indexed: 01/09/2023] Open
Abstract
Precise and fluent genetic manipulation is still limited to only a few prokaryotes. Ideally the highly advanced technologies available in Escherichia coli could be broadly applied. Our efforts to apply lambda Red technology, widely termed ‘recombineering’, in Photorhabdus and Xenorhabdus yielded only limited success. Consequently we explored the properties of an endogenous Photorhabdus luminescens lambda Red-like operon, Plu2934/Plu2935/Plu2936. Bioinformatic and functional tests indicate that Plu2936 is a 5’-3’ exonuclease equivalent to Redα and Plu2935 is a single strand annealing protein equivalent to Redβ. Plu2934 dramatically enhanced recombineering efficiency. Results from bioinformatic analysis and recombineering assays suggest that Plu2934 may be functionally equivalent to Redγ, which inhibits the major endogenous E. coli nuclease, RecBCD. The recombineering utility of Plu2934/Plu2935/Plu2936 was demonstrated by engineering Photorhabdus and Xenorhabdus genomes, including the activation of the 49-kb non-ribosomal peptide synthase (NRPS) gene cluster plu2670 by insertion of a tetracycline inducible promoter. After tetracycline induction, novel secondary metabolites were identified. Our work unlocks the potential for bioprospecting and functional genomics in the Photorhabdus, Xenorhabdus and related genomes.
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Affiliation(s)
- Jia Yin
- Hunan Provincial Key Laboratory for Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, College of Life Science, Hunan Normal University, 410081 Changsha, People's Republic of China
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
- Department of Genomics, Dresden University of Technology, BioInnovations-Zentrum, Tatzberg 47-51, 01307 Dresden, Germany
- Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, PO Box 151150, 66041 Saarbrücken, Germany
| | - Hongbo Zhu
- Department of Protein Evolution, Max-Planck Institute for Developmental Biology, Spemannstr. 35, 72076 Tübingen, Germany
| | - Liqiu Xia
- Hunan Provincial Key Laboratory for Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, College of Life Science, Hunan Normal University, 410081 Changsha, People's Republic of China
| | - Xuezhi Ding
- Hunan Provincial Key Laboratory for Microbial Molecular Biology-State Key Laboratory Breeding Base of Microbial Molecular Biology, College of Life Science, Hunan Normal University, 410081 Changsha, People's Republic of China
| | - Thomas Hoffmann
- Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, PO Box 151150, 66041 Saarbrücken, Germany
| | - Michael Hoffmann
- Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, PO Box 151150, 66041 Saarbrücken, Germany
| | - Xiaoying Bian
- Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, PO Box 151150, 66041 Saarbrücken, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research, Helmholtz Centre for Infection Research and Department of Pharmaceutical Biotechnology, Saarland University, PO Box 151150, 66041 Saarbrücken, Germany
| | - Jun Fu
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
- Department of Genomics, Dresden University of Technology, BioInnovations-Zentrum, Tatzberg 47-51, 01307 Dresden, Germany
| | - A. Francis Stewart
- Department of Genomics, Dresden University of Technology, BioInnovations-Zentrum, Tatzberg 47-51, 01307 Dresden, Germany
| | - Youming Zhang
- Shandong University–Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Shanda Nanlu 27, 250100 Jinan, People's Republic of China
- To whom correspondence should be addressed. Tel: +86 531 88363082; Fax: +86 531 88363203;
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50
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Müller CM, Haase MG, Kemnitz I, Fitze G. Genetic mosaicism of a frameshift mutation in the RET gene in a family with Hirschsprung disease. Gene 2014; 541:51-4. [DOI: 10.1016/j.gene.2014.02.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 02/14/2014] [Indexed: 12/26/2022]
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