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Liu J, He C, Tan W, Zheng JH. Path to bacteriotherapy: From bacterial engineering to therapeutic perspectives. Life Sci 2024; 352:122897. [PMID: 38971366 DOI: 10.1016/j.lfs.2024.122897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 06/30/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
The major reason for the failure of conventional therapies is the heterogeneity and complexity of tumor microenvironments (TMEs). Many malignant tumors reprogram their surface antigens to evade the immune surveillance, leading to reduced antigen-presenting cells and hindered T-cell activation. Bacteria-mediated cancer immunotherapy has been extensively investigated in recent years. Scientists have ingeniously modified bacteria using synthetic biology and nanotechnology to enhance their biosafety with high tumor specificity, resulting in robust anticancer immune responses. To enhance the antitumor efficacy, therapeutic proteins, cytokines, nanoparticles, and chemotherapeutic drugs have been efficiently delivered using engineered bacteria. This review provides a comprehensive understanding of oncolytic bacterial therapies, covering bacterial design and the intricate interactions within TMEs. Additionally, it offers an in-depth comparison of the current techniques used for bacterial modification, both internally and externally, to maximize their therapeutic effectiveness. Finally, we outlined the challenges and opportunities ahead in the clinical application of oncolytic bacterial therapies.
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Affiliation(s)
- Jinling Liu
- The Affiliated Xiangtan Central Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha 410082, China; College of Biology, Hunan University, Changsha 410082, China
| | - Chongsheng He
- College of Biology, Hunan University, Changsha 410082, China
| | - Wenzhi Tan
- School of Food Science and Bioengineering, Changsha University of Science & Technology, Changsha, Hunan 410114, China.
| | - Jin Hai Zheng
- The Affiliated Xiangtan Central Hospital of Hunan University, School of Biomedical Sciences, Hunan University, Changsha 410082, China.
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2
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Huang X, Tang Q, Liu S, Li C, Li Y, Sun Y, Ding X, Xia L, Hu S. Discovery of an antitumor compound from xenorhabdus stockiae HN_xs01. World J Microbiol Biotechnol 2024; 40:101. [PMID: 38366186 DOI: 10.1007/s11274-024-03915-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 02/01/2024] [Indexed: 02/18/2024]
Abstract
Xenorhabdus, known for its symbiotic relationship with Entomopathogenic nematodes (EPNs), belongs to the Enterobacteriaceae family. This dual-host symbiotic nematode exhibits pathogenic traits, rendering it a promising biocontrol agent against insects. Our prior investigations revealed that Xenorhabdus stockiae HN_xs01, isolated in our laboratory, demonstrates exceptional potential in halting bacterial growth and displaying anti-tumor activity. Subsequently, we separated and purified the supernatant of the HN_xs01 strain and obtained a new compound with significant inhibitory activity on tumor cells, which we named XNAE. Through LC-MS analysis, the mass-to-nucleus ratio of XNAE was determined to be 254.24. Our findings indicated that XNAE exerts a time- and dose-dependent inhibition on B16 and HeLa cells. After 24 h, its IC50 for B16 and HeLa cells was 30.178 µg/mL and 33.015 µg/mL, respectively. Electron microscopy revealed conspicuous damage to subcellular structures, notably mitochondria and the cytoskeleton, resulting in a notable reduction in cell numbers among treated tumor cells. Interestingly, while XNAE exerted a more pronounced inhibitory effect on B16 cells compared to HeLa cells, it showed no discernible impact on HUVEC cells. Treatment of B16 cells with XNAE induced early apoptosis and led to cell cycle arrest in the G2 phase, as evidenced by flow cytometry analysis. The impressive capability of X. stockiae HN_xs01 in synthesizing bioactive secondary metabolites promises to significantly expand the reservoir of natural products. Further exploration to identify the bioactivity of these compounds holds the potential to shed light on their roles in bacteria-host interaction. Overall, these outcomes underscore the promising potential of XNAE as a bioactive compound for tumor treatment.
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Affiliation(s)
- Xiyin Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, No.36 Lushan Street, Changsha, 410081, China
| | - Qiong Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, No.36 Lushan Street, Changsha, 410081, China
| | - Siqin Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, No.36 Lushan Street, Changsha, 410081, China
| | - Chen Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, No.36 Lushan Street, Changsha, 410081, China
| | - Yaoguang Li
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, No.36 Lushan Street, Changsha, 410081, China
| | - Yunjun Sun
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, No.36 Lushan Street, Changsha, 410081, China
| | - Xuezhi Ding
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, No.36 Lushan Street, Changsha, 410081, China
| | - Liqiu Xia
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, No.36 Lushan Street, Changsha, 410081, China
| | - Shengbiao Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Provincial Key Laboratory of Microbial Molecular Biology, College of Life Science, Hunan Normal University, No.36 Lushan Street, Changsha, 410081, China.
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3
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Trujillo Rodríguez L, Ellington AJ, Reisch CR, Chevrette MG. CRISPR-Associated Transposase for Targeted Mutagenesis in Diverse Proteobacteria. ACS Synth Biol 2023. [PMID: 37368499 PMCID: PMC10367135 DOI: 10.1021/acssynbio.3c00065] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
Abstract
Genome editing tools, through the disruption of an organism's native genetic material or the introduction of non-native DNA, facilitate functional investigations to link genotypes to phenotypes. Transposons have been instrumental genetic tools in microbiology, enabling genome-wide, randomized disruption of genes and insertions of new genetic elements. Due to this randomness, identifying and isolating particular transposon mutants (i.e., those with modifications at a genetic locus of interest) can be laborious, often requiring one to sift through hundreds or thousands of mutants. Programmable, site-specific targeting of transposons became possible with recently described CRISPR-associated transposase (CASTs) systems, allowing the streamlined recovery of desired mutants in a single step. Like other CRISPR-derived systems, CASTs can be programmed by guide-RNA that is transcribed from short DNA sequence(s). Here, we describe a CAST system and demonstrate its function in bacteria from three classes of Proteobacteria. A dual plasmid strategy is demonstrated: (i) CAST genes are expressed from a broad-host-range replicative plasmid and (ii) guide-RNA and transposon are encoded on a high-copy, suicidal pUC plasmid. Using our CAST system, single-gene disruptions were performed with on-target efficiencies approaching 100% in Beta- and Gammaproteobacteria (Burkholderia thailandensis and Pseudomonas putida, respectively). We also report a peak efficiency of 45% in the Alphaproteobacterium Agrobacterium fabrum. In B. thailandensis, we performed simultaneous co-integration of transposons at two different target sites, demonstrating CAST's utility in multilocus strategies. The CAST system is also capable of high-efficiency large transposon insertion totaling over 11 kbp in all three bacteria tested. Lastly, the dual plasmid system allowed for iterative transposon mutagenesis in all three bacteria without loss of efficiency. Given these iterative capabilities and large payload capacity, this system will be helpful for genome engineering experiments across several fields of research.
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Affiliation(s)
- Lidimarie Trujillo Rodríguez
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida 32611, United States
| | - Adam J Ellington
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida 32611, United States
| | - Christopher R Reisch
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida 32611, United States
| | - Marc G Chevrette
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida 32611, United States
- University of Florida Genetics Institute, Gainesville, Florida 32610, United States
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4
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Huang X, Sun Y, Liu S, Li Y, Li C, Sun Y, Ding X, Xia L, Hu Y, Hu S. Recombineering using RecET-like recombinases from Xenorhabdus and its application in mining of natural products. Appl Microbiol Biotechnol 2022; 106:7857-7866. [DOI: 10.1007/s00253-022-12258-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 10/14/2022] [Accepted: 10/23/2022] [Indexed: 11/06/2022]
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Bertram R, Neumann B, Schuster CF. Status quo of tet regulation in bacteria. Microb Biotechnol 2022; 15:1101-1119. [PMID: 34713957 PMCID: PMC8966031 DOI: 10.1111/1751-7915.13926] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/02/2021] [Accepted: 09/04/2021] [Indexed: 11/27/2022] Open
Abstract
The tetracycline repressor (TetR) belongs to the most popular, versatile and efficient transcriptional regulators used in bacterial genetics. In the tetracycline (Tc) resistance determinant tet(B) of transposon Tn10, tetR regulates the expression of a divergently oriented tetA gene that encodes a Tc antiporter. These components of Tn10 and of other natural or synthetic origins have been used for tetracycline-dependent gene regulation (tet regulation) in at least 40 bacterial genera. Tet regulation serves several purposes such as conditional complementation, depletion of essential genes, modulation of artificial genetic networks, protein overexpression or the control of gene expression within cell culture or animal infection models. Adaptations of the promoters employed have increased tet regulation efficiency and have made this system accessible to taxonomically distant bacteria. Variations of TetR, different effector molecules and mutated DNA binding sites have enabled new modes of gene expression control. This article provides a current overview of tet regulation in bacteria.
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Affiliation(s)
- Ralph Bertram
- Institute of Clinical Hygiene, Medical Microbiology and InfectiologyParacelsus Medical UniversityProf.‐Ernst‐Nathan‐Straße 1Nuremberg90419Germany
| | - Bernd Neumann
- Institute of Clinical Hygiene, Medical Microbiology and InfectiologyParacelsus Medical UniversityProf.‐Ernst‐Nathan‐Straße 1Nuremberg90419Germany
| | - Christopher F. Schuster
- Department of Infectious DiseasesDivision of Nosocomial Pathogens and Antibiotic ResistancesRobert Koch InstituteBurgstraße 37Wernigerode38855Germany
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6
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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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7
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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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8
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Qian Y, Kong W, Lu T. Precise and reliable control of gene expression in Agrobacterium tumefaciens. Biotechnol Bioeng 2021; 118:3962-3972. [PMID: 34180537 DOI: 10.1002/bit.27872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/07/2021] [Accepted: 06/17/2021] [Indexed: 11/07/2022]
Abstract
Agrobacterium tumefaciens is a soil-borne bacterium that is known for its DNA delivery ability and widely exploited for plant transformation. Despite continued interest in improving the utility of the organism, the lack of well-characterized engineering tools limits the realization of its full potential. Here, we present a synthetic biology toolkit that enables precise and effective control of gene expression in A. tumefaciens. We constructed and characterized six inducible expression systems. Then, we optimized the one regulated by cumic acid through amplifier introduction and promoter engineering and evaluated its 15 cognate promoters. To establish fine-tunability, we constructed a series of spacers and a promoter library to systematically modulate both translational and transcriptional rates. We finally demonstrated the application of the tools by co-expressing genes with altered expression levels using a single signal. This study provides precise expression tools for A. tumefaciens, facilitating rational engineering of the bacterium for advanced plant biotechnological applications.
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Affiliation(s)
- Yuanchao Qian
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Wentao Kong
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ting Lu
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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9
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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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10
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Abstract
Agrobacterium spp. are important plant pathogens that are the causative agents of crown gall or hairy root disease. Their unique infection strategy depends on the delivery of part of their DNA to plant cells. Thanks to this capacity, these phytopathogens became a powerful and indispensable tool for plant genetic engineering and agricultural biotechnology. Although Agrobacterium spp. are standard tools for plant molecular biologists, current laboratory strains have remained unchanged for decades and functional gene analysis of Agrobacterium has been hampered by time-consuming mutation strategies. Here, we developed clustered regularly interspaced short palindromic repeats (CRISPR)-mediated base editing to enable the efficient introduction of targeted point mutations into the genomes of both Agrobacterium tumefaciens and Agrobacterium rhizogenes As an example, we generated EHA105 strains with loss-of-function mutations in recA, which were fully functional for maize (Zea mays) transformation and confirmed the importance of RolB and RolC for hairy root development by A. rhizogenes K599. Our method is highly effective in 9 of 10 colonies after transformation, with edits in at least 80% of the cells. The genomes of EHA105 and K599 were resequenced, and genome-wide off-target analysis was applied to investigate the edited strains after curing of the base editor plasmid. The off-targets present were characteristic of Cas9-independent off-targeting and point to TC motifs as activity hotspots of the cytidine deaminase used. We anticipate that CRISPR-mediated base editing is the start of "engineering the engineer," leading to improved Agrobacterium strains for more efficient plant transformation and gene editing.
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11
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CRISPR-Cas-mediated gene editing in lactic acid bacteria. Mol Biol Rep 2020; 47:8133-8144. [PMID: 32926267 DOI: 10.1007/s11033-020-05820-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 09/05/2020] [Indexed: 12/12/2022]
Abstract
The high efficiency, convenience and diversity of clustered regular interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) systems are driving a technological revolution in the gene editing of lactic acid bacteria (LAB). Cas-RNA cassettes have been adopted as tools to perform gene deletion, insertion and point mutation in several species of LAB. In this article, we describe the basic mechanisms of the CRISPR-Cas system, and the current gene editing methods available, focusing on the CRISPR-Cas models developed for LAB. We also compare the different types of CRISPR-Cas-based genomic manipulations classified according to the different Cas proteins and the type of recombineering, and discuss the rapidly evolving landscape of CRISPR-Cas application in LAB.
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12
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Fels U, Gevaert K, Van Damme P. Bacterial Genetic Engineering by Means of Recombineering for Reverse Genetics. Front Microbiol 2020; 11:548410. [PMID: 33013782 PMCID: PMC7516269 DOI: 10.3389/fmicb.2020.548410] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 08/14/2020] [Indexed: 12/11/2022] Open
Abstract
Serving a robust platform for reverse genetics enabling the in vivo study of gene functions primarily in enterobacteriaceae, recombineering -or recombination-mediated genetic engineering-represents a powerful and relative straightforward genetic engineering tool. Catalyzed by components of bacteriophage-encoded homologous recombination systems and only requiring short ∼40–50 base homologies, the targeted and precise introduction of modifications (e.g., deletions, knockouts, insertions and point mutations) into the chromosome and other episomal replicons is empowered. Furthermore, by its ability to make use of both double- and single-stranded linear DNA editing substrates (e.g., PCR products or oligonucleotides, respectively), lengthy subcloning of specific DNA sequences is circumvented. Further, the more recent implementation of CRISPR-associated endonucleases has allowed for more efficient screening of successful recombinants by the selective purging of non-edited cells, as well as the creation of markerless and scarless mutants. In this review we discuss various recombineering strategies to promote different types of gene modifications, how they are best applied, and their possible pitfalls.
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Affiliation(s)
- Ursula Fels
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
| | - Kris Gevaert
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Petra Van Damme
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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13
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Abbasi MN, Fu J, Bian X, Wang H, Zhang Y, Li A. Recombineering for Genetic Engineering of Natural Product Biosynthetic Pathways. Trends Biotechnol 2020; 38:715-728. [PMID: 31973879 DOI: 10.1016/j.tibtech.2019.12.018] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 12/11/2019] [Accepted: 12/12/2019] [Indexed: 01/21/2023]
Abstract
Microbial genomes encode many cryptic and uncharacterized biosynthetic gene clusters (BGCs). Exploiting this unexplored genetic wealth to discover microbial novel natural products (NPs) remains a challenging issue. We review homologous recombination (HR)-based recombineering, mediated by the recombinases RecE/RecT from Rac prophage and Redα/Redβ from lambda phage, which has developed into a highly inclusive tool for direct cloning of large DNA up to 100 kb, seamless mutation, multifragment assembly, and heterologous expression of microbial NP BGCs. Its utilization in the refactoring, engineering, and functional expression of long BGCs for NP biosynthesis makes it easy to elucidate NP-producing potential in microbes. This review also highlights various applications of recombineering in NP-derived drug discovery.
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Affiliation(s)
- Muhammad Nazeer Abbasi
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Jun Fu
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR 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, PR China
| | - Hailong Wang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
| | - Youming Zhang
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
| | - Aiying Li
- Helmholtz International Lab for Anti-Infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
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14
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CRISPR/Cas9-Assisted Seamless Genome Editing in Lactobacillus plantarum and Its Application in N-Acetylglucosamine Production. Appl Environ Microbiol 2019; 85:AEM.01367-19. [PMID: 31444197 DOI: 10.1128/aem.01367-19] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 08/14/2019] [Indexed: 12/30/2022] Open
Abstract
Lactobacillus plantarum is a potential starter and health-promoting probiotic bacterium. Effective, precise, and diverse genome editing of Lactobacillus plantarum without introducing exogenous genes or plasmids is of great importance. In this study, CRISPR/Cas9-assisted double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) recombineering was established in L. plantarum WCFS1 to seamlessly edit the genome, including gene knockouts, insertions, and point mutations. To optimize our editing method, phosphorothioate modification was used to improve the dsDNA insertion, and adenine-specific methyltransferase was used to improve the ssDNA recombination efficiency. These strategies were applied to engineer L. plantarum WCFS1 toward producing N-acetylglucosamine (GlcNAc). nagB was truncated to eliminate the reverse reaction of fructose-6-phosphate (F6P) to glucosamine 6-phosphate (GlcN-6P). Riboswitch replacement and point mutation in glmS1 were introduced to relieve feedback repression. The resulting strain produced 797.3 mg/liter GlcNAc without introducing exogenous genes or plasmids. This strategy may contribute to the available methods for precise and diverse genetic engineering in lactic acid bacteria and boost strain engineering for more applications.IMPORTANCE CRISPR/Cas9-assisted recombineering is restricted in lactic acid bacteria because of the lack of available antibiotics and vectors. In this study, a seamless genome editing method was carried out in Lactobacillus plantarum using CRISPR/Cas9-assisted double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) recombineering, and recombination efficiency was effectively improved by endogenous adenine-specific methyltransferase overexpression. L. plantarum WCFS1 produced 797.3 mg/liter N-acetylglucosamine (GlcNAc) through reinforcement of the GlcNAc pathway, without introducing exogenous genes or plasmids. This seamless editing strategy, combined with the potential exogenous GlcNAc-producing pathway, makes this strain an attractive candidate for industrial use in the future.
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15
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Corts AD, Thomason LC, Gill RT, Gralnick JA. A new recombineering system for precise genome-editing in Shewanella oneidensis strain MR-1 using single-stranded oligonucleotides. Sci Rep 2019; 9:39. [PMID: 30631105 PMCID: PMC6328582 DOI: 10.1038/s41598-018-37025-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 11/27/2018] [Indexed: 11/09/2022] Open
Abstract
Shewanella oneidensis MR-1 is an invaluable host for the discovery and engineering of pathways important for bioremediation of toxic and radioactive metals and understanding extracellular electron transfer. However, genetic manipulation is challenging due to the lack of genetic tools. Previously, the only reliable method used for introducing DNA into Shewanella spp. at high efficiency was bacterial conjugation, enabling transposon mutagenesis and targeted knockouts using suicide vectors for gene disruptions. Here, we describe development of a robust and simple electroporation method in S. oneidensis that allows an efficiency of ~4.0 x 106 transformants/µg DNA. High transformation efficiency is maintained when cells are frozen for long term storage. In addition, we report a new prophage-mediated genome engineering (recombineering) system using a λ Red Beta homolog from Shewanella sp. W3-18-1. By targeting two different chromosomal alleles, we demonstrate its application for precise genome editing using single strand DNA oligonucleotides and show that an efficiency of ~5% recombinants among total cells can be obtained. This is the first effective and simple strategy for recombination with markerless mutations in S. oneidensis. Continued development of this recombinant technology will advance high-throughput and genome modification efforts to engineer and investigate S. oneidensis and other environmental bacteria.
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Affiliation(s)
- Anna D Corts
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, MN, 55108, USA
| | - Lynn C Thomason
- RNA Biology Laboratory, Basic Science Program, Leidos Biomedical Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA
| | - Ryan T Gill
- Department of Chemical and Biological Engineering, University of Colorado-Boulder, Boulder, CO, 80303, USA
| | - Jeffrey A Gralnick
- BioTechnology Institute and Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, MN, 55108, USA.
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16
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Murphy KC, Nelson SJ, Nambi S, Papavinasasundaram K, Baer CE, Sassetti CM. ORBIT: a New Paradigm for Genetic Engineering of Mycobacterial Chromosomes. mBio 2018; 9:e01467-18. [PMID: 30538179 PMCID: PMC6299477 DOI: 10.1128/mbio.01467-18] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/19/2018] [Indexed: 11/20/2022] Open
Abstract
Two efficient recombination systems were combined to produce a versatile method for chromosomal engineering that obviates the need to prepare double-stranded DNA (dsDNA) recombination substrates. A synthetic "targeting oligonucleotide" is incorporated into the chromosome via homologous recombination mediated by the phage Che9c RecT annealase. This oligonucleotide contains a site-specific recombination site for the directional Bxb1 integrase (Int), which allows the simultaneous integration of a "payload plasmid" that contains a cognate recombination site and a selectable marker. The targeting oligonucleotide and payload plasmid are cotransformed into a RecT- and Int-expressing strain, and drug-resistant homologous recombinants are selected in a single step. A library of reusable target-independent payload plasmids is available to generate gene knockouts, promoter replacements, or C-terminal tags. This new system is called ORBIT (for "oligonucleotide-mediated recombineering followed by Bxb1 integrase targeting") and is ideally suited for the creation of libraries consisting of large numbers of deletions, insertions, or fusions in a bacterial chromosome. We demonstrate the utility of this "drag and drop" strategy by the construction of insertions or deletions in over 100 genes in Mycobacteriumtuberculosis and M. smegmatisIMPORTANCE We sought to develop a system that could increase the usefulness of oligonucleotide-mediated recombineering of bacterial chromosomes by expanding the types of modifications generated by an oligonucleotide (i.e., insertions and deletions) and by making recombinant formation a selectable event. This paper describes such a system for use in M. smegmatis and M. tuberculosis By incorporating a single-stranded DNA (ssDNA) version of the phage Bxb1 attP site into the oligonucleotide and coelectroporating it with a nonreplicative plasmid that carries an attB site and a drug selection marker, we show both formation of a chromosomal attP site and integration of the plasmid in a single transformation. No target-specific dsDNA substrates are required. This system will allow investigators studying mycobacterial diseases, including tuberculosis, to easily generate multiple mutants for analysis of virulence factors, identification of new drug targets, and development of new vaccines.
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Affiliation(s)
- Kenan C Murphy
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Samantha J Nelson
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Subhalaxmi Nambi
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Kadamba Papavinasasundaram
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Christina E Baer
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Christopher M Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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17
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Discovery of recombinases enables genome mining of cryptic biosynthetic gene clusters in Burkholderiales species. Proc Natl Acad Sci U S A 2018; 115:E4255-E4263. [PMID: 29666226 PMCID: PMC5939090 DOI: 10.1073/pnas.1720941115] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Natural products biosynthesized by cryptic gene clusters represent a largely untapped source for drug discovery. However, mining of these products by promoter engineering is restricted by the lack of streamlined genetic tools, especially in nonmodel biosynthetic gene cluster (BGC)-rich bacteria. Here, we describe the discovery of a pair of bacteriophage recombinases and application of recombinase-assisted promoter engineering to rapidly identify and activate several cryptic biosynthetic gene clusters in two Burkholderiales strains that currently lack effective genetic tools. Construction of an efficient genome engineering platform in a natural product producer expedites mining of cryptic BGCs in their native backgrounds, and host melioration for yield or structure optimization. This strategy enables potentially scalable discovery of novel metabolites with intriguing bioactivities from many other bacteria. Bacterial genomes encode numerous cryptic biosynthetic gene clusters (BGCs) that represent a largely untapped source of drugs or pesticides. Mining of the cryptic products is limited by the unavailability of streamlined genetic tools in native producers. Precise genome engineering using bacteriophage recombinases is particularly useful for genome mining. However, recombinases are usually host-specific. The genome-guided discovery of novel recombinases and their transient expression could boost cryptic BGC mining. Herein, we reported a genetic system employing Red recombinases from Burkholderiales strain DSM 7029 for efficient genome engineering in several Burkholderiales species that currently lack effective genetic tools. Using specialized recombinases-assisted in situ insertion of functional promoters, we successfully mined five cryptic nonribosomal peptide synthetase/polyketide synthase BGCs, two of which were silent. Two classes of lipopeptides, glidopeptins and rhizomides, were identified through extensive spectroscopic characterization. This recombinase expression strategy offers utility within other bacteria species, allowing bioprospecting for potentially scalable discovery of novel metabolites with attractive bioactivities.
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18
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Xin Y, Guo T, Mu Y, Kong J. Identification and functional analysis of potential prophage-derived recombinases for genome editing in Lactobacillus casei. FEMS Microbiol Lett 2017; 364:4628040. [DOI: 10.1093/femsle/fnx243] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 11/13/2017] [Indexed: 12/16/2022] Open
Affiliation(s)
- Yongping Xin
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, P. R. China
| | - Tingting Guo
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, P. R. China
| | - Yingli Mu
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, P. R. China
| | - Jian Kong
- State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, P. R. China
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19
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Ekandjo LK, Ruppel S, Remus R, Witzel K, Patz S, Becker Y. Site-directed mutagenesis to deactivate two nitrogenase isozymes of Kosakonia radicincitans DSM16656 T. Can J Microbiol 2017; 64:97-106. [PMID: 29059532 DOI: 10.1139/cjm-2017-0532] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Biological nitrogen fixation (BNF) is considered one of the key plant-growth-promoting (PGP) factors for diazotrophic organisms. Whether the iron and iron-molybdenum nitrogenases of Kosakonia radicincitans contribute to its PGP effect is yet to be proven. Hence, for the first time, we conducted site-directed mutagenesis in K. radicincitans to knock out anfH and (or) nifH as a mean to deactivate BNF in this strain. We used 15N2-labeled air to trace BNF activities in ΔanfH, ΔnifH, and ΔanfHΔnifH mutants. Assessing bacterial growth, nitrogen content, and 15N incorporation revealed that BNF is impaired in K. radicincitans DSM16656T ΔnifH and ΔanfHΔnifH. However, we detected no significant contribution of the Fe nitrogenase to biological dinitrogen assimilation under our pure bacterial culture experimental conditions. Such nondiazotrophic K. radicincitans DSM16656T mutants represent excellent tools for investigating nitrogen nutrition in K. radicincitans-inoculated plants.
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Affiliation(s)
- Lempie K Ekandjo
- a Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Groβbeeren, Germany
| | - Silke Ruppel
- a Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Groβbeeren, Germany
| | - Rainer Remus
- b Leibniz Centre for Agricultural Landscape Research, Eberswalder Straβe 84, 15374 Müncheberg, Germany
| | - Katja Witzel
- a Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Groβbeeren, Germany
| | - Sascha Patz
- a Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Groβbeeren, Germany
| | - Yvonne Becker
- a Leibniz Institute of Vegetable and Ornamental Crops, Theodor-Echtermeyer-Weg 1, 14979 Groβbeeren, Germany
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20
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Subramaniam S, Erler A, Fu J, Kranz A, Tang J, Gopalswamy M, Ramakrishnan S, Keller A, Grundmeier G, Müller D, Sattler M, Stewart AF. DNA annealing by Redβ is insufficient for homologous recombination and the additional requirements involve intra- and inter-molecular interactions. Sci Rep 2016; 6:34525. [PMID: 27708411 PMCID: PMC5052646 DOI: 10.1038/srep34525] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 08/15/2016] [Indexed: 01/09/2023] Open
Abstract
Single strand annealing proteins (SSAPs) like Redβ initiate homologous recombination by annealing complementary DNA strands. We show that C-terminally truncated Redβ, whilst still able to promote annealing and nucleoprotein filament formation, is unable to mediate homologous recombination. Mutations of the C-terminal domain were evaluated using both single- and double stranded (ss and ds) substrates in recombination assays. Mutations of critical amino acids affected either dsDNA recombination or both ssDNA and dsDNA recombination indicating two separable functions, one of which is critical for dsDNA recombination and the second for recombination per se. As evaluated by co-immunoprecipitation experiments, the dsDNA recombination function relates to the Redα-Redβ protein-protein interaction, which requires not only contacts in the C-terminal domain but also a region near the N-terminus. Because the nucleoprotein filament formed with C-terminally truncated Redβ has altered properties, the second C-terminal function could be due to an interaction required for functional filaments. Alternatively the second C-terminal function could indicate a requirement for a Redβ-host factor interaction. These data further advance the model for Red recombination and the proposition that Redβ and RAD52 SSAPs share ancestral and mechanistic roots.
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Affiliation(s)
| | - Axel Erler
- Genomics, Biotechnology Center, TU Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Jun Fu
- Genomics, Biotechnology Center, TU Dresden, Tatzberg 47/49, 01307 Dresden, 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
| | - Andrea Kranz
- Genomics, Biotechnology Center, TU Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Jing Tang
- Genomics, Biotechnology Center, TU Dresden, Tatzberg 47/49, 01307 Dresden, Germany
| | - Mohanraj Gopalswamy
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany and Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstr.4, 85747 Garching, Germany
| | - Saminathan Ramakrishnan
- Technical and Macromolecular Chemistry, University of Paderborn, Warburger Str. 100 33098 Paderborn, Germany
| | - Adrian Keller
- Technical and Macromolecular Chemistry, University of Paderborn, Warburger Str. 100 33098 Paderborn, Germany
| | - Guido Grundmeier
- Technical and Macromolecular Chemistry, University of Paderborn, Warburger Str. 100 33098 Paderborn, Germany
| | - Daniel Müller
- Department of Biosystems Science and Engineering (D-BSSE), ETH Zürich, Mattenstraße 26, 4058 Basel, Switzerland
| | - Michael Sattler
- Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg, Germany and Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry, Technische Universität München, Lichtenbergstr.4, 85747 Garching, Germany
| | - A Francis Stewart
- Genomics, Biotechnology Center, TU Dresden, Tatzberg 47/49, 01307 Dresden, Germany
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21
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Abstract
The bacteriophage λ Red homologous recombination system has been studied over the past 50 years as a model system to define the mechanistic details of how organisms exchange DNA segments that share extended regions of homology. The λ Red system proved useful as a system to study because recombinants could be easily generated by co-infection of genetically marked phages. What emerged from these studies was the recognition that replication of phage DNA was required for substantial Red-promoted recombination in vivo, and the critical role that double-stranded DNA ends play in allowing the Red proteins access to the phage DNA chromosomes. In the past 16 years, however, the λ Red recombination system has gained a new notoriety. When expressed independently of other λ functions, the Red system is able to promote recombination of linear DNA containing limited regions of homology (∼50 bp) with the Escherichia coli chromosome, a process known as recombineering. This review explains how the Red system works during a phage infection, and how it is utilized to make chromosomal modifications of E. coli with such efficiency that it changed the nature and number of genetic manipulations possible, leading to advances in bacterial genomics, metabolic engineering, and eukaryotic genetics.
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Affiliation(s)
- Kenan C Murphy
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01605
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22
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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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Efficient Construction of Large Genomic Deletion in Agrobacterium tumefaciens by Combination of Cre/loxP System and Triple Recombineering. Curr Microbiol 2016; 72:465-72. [DOI: 10.1007/s00284-015-0977-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Accepted: 11/25/2015] [Indexed: 10/22/2022]
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Yang P, Wang J, Qi Q. Prophage recombinases-mediated genome engineering in Lactobacillus plantarum. Microb Cell Fact 2015; 14:154. [PMID: 26438232 PMCID: PMC4595204 DOI: 10.1186/s12934-015-0344-z] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 09/18/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Lactobacillus plantarum is a food-grade microorganism with industrial and medical relevance belonging to the group of lactic acid bacteria (LAB). Traditional strategies for obtaining gene deletion variants in this organism are mainly vector-based double-crossover methods, which are inefficient and laborious. A feasible possibility to solve this problem is the recombineering, which greatly expands the possibilities for engineering DNA molecules in vivo in various organisms. RESULTS In this work, a double-stranded DNA (dsDNA) recombineering system was established in L. plantarum. An exonuclease encoded by lp_0642 and a potential host-nuclease inhibitor encoded by lp_0640 involved in dsDNA recombination were identified from a prophage P1 locus in L. plantarum WCFS1. These two proteins, combined with the previously characterized single strand annealing protein encoded by lp_0641, can perform homologous recombination between a heterologous dsDNA substrate and host genomic DNA. Based on this, we developed a method for marker-free genetic manipulation of the chromosome in L. plantarum. CONCLUSIONS This Lp_0640-41-42-mediated recombination allowed easy screening of mutants and could serve as an alternative to other genetic manipulation methods. We expect that this method can help for understanding the probiotic functionality and physiology of LAB.
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Affiliation(s)
- Peng Yang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, People's Republic of China.
| | - Jing Wang
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, People's Republic of China.
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, People's Republic of China.
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25
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Biswas I. Genetic tools for manipulating Acinetobacter baumannii genome: an overview. J Med Microbiol 2015; 64:657-669. [PMID: 25948809 DOI: 10.1099/jmm.0.000081] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Acinetobacter baumannii is an emerging nosocomial pathogen involved in a variety of infections ranging from minor soft-tissue infections to more severe infections such as ventilator-associated pneumonia and bacteraemia. A. baumannii has become resistant to most of the commonly used antibiotics and multidrug-resistant isolates are becoming a severe problem in the healthcare setting. In the past few years, whole-genome sequences of >200 A. baumannii isolates have been generated. Several methods and molecular tools have been used for genetic manipulation of various Acinetobacter spp. Here, we review recent developments of various genetic tools used for modification of the A. baumannii genome, including various ways to inactivate gene function, chromosomal integration and transposon mutagenesis.
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Affiliation(s)
- Indranil Biswas
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS 66160, USA
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26
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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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Nakayama H, Shimamoto N. Modern and simple construction of plasmid: saving time and cost. J Microbiol 2014; 52:891-7. [PMID: 25359266 DOI: 10.1007/s12275-014-4501-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 09/15/2014] [Indexed: 12/26/2022]
Abstract
Construction of plasmids has been occupying a significant fraction of laboratory work in most fields of experimental biology. Tremendous effort was made to improve the traditional method for constructing plasmids, in which DNA fragments digested with restriction enzymes were ligated. However, the traditional method remained to be a standard protocol more than 40 years. At last, several recent inventions are rapidly and completely replacing the traditional method, because they are far quicker with less cost, and requiring less material. We here introduce three such methods that cover up most of the cases. Moreover, they are complementary with each other. Our lab protocols are provided for "no strain, no pain" construction of plasmids.
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Affiliation(s)
- Hideki Nakayama
- Faculty of Life Sciences, Kyoto Sangyo University, Kamigamo-Motoyama, Kita-Ku, Kyoto, 603-8555, Japan
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