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Hadjadj L, Baron SA, Diene SM, Rolain JM. How to discover new antibiotic resistance genes? Expert Rev Mol Diagn 2019; 19:349-362. [PMID: 30895843 DOI: 10.1080/14737159.2019.1592678] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
INTRODUCTION Antibiotic resistance (AR) is a worldwide concern and the description of AR have been discovered mainly because of their implications in human medicine. Since the recent burden of whole-genome sequencing of microorganisms, the number of new AR genes (ARGs) have dramatically increased over the last decade. Areas covered: In this review, we will describe the different methods that could be used to characterize new ARGs using classic or innovative methods. First, we will focus on the biochemical methods, then we will develop on molecular methods, next-generation sequencing and bioinformatics approaches. The use of various methods, including cloning, mutagenesis, transposon mutagenesis, functional genomics, whole genome sequencing, metagenomic and functional metagenomics will be reviewed here, outlining the advantages and drawbacks of each method. Bioinformatics softwares used for resistome analysis and protein modeling will be also described. Expert opinion: Biological experiments and bioinformatics analysis are complementary. Nowadays, the ARGs described only account for the tip of the iceberg of all existing resistance mechanisms. The multiplication of the ecosystems studied allows us to find a large reservoir of AR mechanisms. Furthermore, the adaptation ability of bacteria facing new antibiotics promises a constant discovery of new AR mechanisms.
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Affiliation(s)
- Linda Hadjadj
- a Microbes Evolution Phylogeny and Infections (MEPHI), IRD, APHM, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille-Univ , Marseille , France
| | - Sophie Alexandra Baron
- a Microbes Evolution Phylogeny and Infections (MEPHI), IRD, APHM, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille-Univ , Marseille , France
| | - Seydina M Diene
- a Microbes Evolution Phylogeny and Infections (MEPHI), IRD, APHM, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille-Univ , Marseille , France
| | - Jean-Marc Rolain
- a Microbes Evolution Phylogeny and Infections (MEPHI), IRD, APHM, IHU Méditerranée Infection, Faculté de Médecine et de Pharmacie , Aix-Marseille-Univ , Marseille , France.,b IHU Méditerranée Infection , Marseille , France
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Liang Y, Zeng X, Peng X, Hou X. Arabidopsis glutamate:glyoxylate aminotransferase 1 (Ler) mutants generated by CRISPR/Cas9 and their characteristics. Transgenic Res 2018; 27:61-74. [DOI: 10.1007/s11248-017-0052-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 11/27/2017] [Indexed: 10/18/2022]
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Applications of the Bacteriophage Mu In Vitro Transposition Reaction and Genome Manipulation via Electroporation of DNA Transposition Complexes. Methods Mol Biol 2018; 1681:279-286. [PMID: 29134602 DOI: 10.1007/978-1-4939-7343-9_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The capacity of transposable elements to insert into the genomes has been harnessed during the past decades to various in vitro and in vivo applications. This chapter describes in detail the general protocols and principles applicable for the Mu in vitro transposition reaction as well as the assembly of DNA transposition complexes that can be electroporated into bacterial cells to accomplish efficient gene delivery. These techniques with their modifications potentiate various gene and genome modification applications, which are discussed briefly here, and the reader is referred to the original publications for further details.
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Pulkkinen E, Haapa-Paananen S, Savilahti H. An assay to monitor the activity of DNA transposition complexes yields a general quality control measure for transpositional recombination reactions. Mob Genet Elements 2014; 4:1-8. [PMID: 26442171 PMCID: PMC4590003 DOI: 10.4161/21592543.2014.969576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 08/22/2014] [Accepted: 09/01/2014] [Indexed: 12/20/2022] Open
Abstract
Transposon-based technologies have many applications in molecular biology and can be used for gene delivery into prokaryotic and eukaryotic cells. Common transpositional activity measurement assays suitable for many types of transposons would be beneficial, as diverse transposon systems could be compared for their performance attributes. Therefore, we developed a general-purpose assay to enable and standardize the activity measurement for DNA transposition complexes (transpososomes), using phage Mu transposition as a test platform. This assay quantifies transpositional recombination efficiency and is based on an in vitro transposition reaction with a target plasmid carrying a lethal ccdB gene. If transposition targets ccdB, this gene becomes inactivated, enabling plasmid-receiving Escherichia coli cells to survive and to be scored as colonies on selection plates. The assay was validated with 3 mini-Mu transposons varying in size and differing in their marker gene constitution. Tests with different amounts of transposon DNA provided a linear response and yielded a 10-fold operational range for the assay. The colony formation capacity was linearly correlated with the competence status of the E.coli cells, enabling normalization of experimental data obtained with different batches of recipient cells. The developed assay can now be used to directly compare transpososome activities with all types of mini-Mu transposons, regardless of their aimed use. Furthermore, the assay should be directly applicable to other transposition-based systems with a functional in vitro reaction, and it provides a dependable quality control measure that previously has been lacking but is highly important for the evaluation of current and emerging transposon-based applications.
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Affiliation(s)
- Elsi Pulkkinen
- Division of Genetics and Physiology; Department of Biology; University of Turku; Turku, Finland
| | - Saija Haapa-Paananen
- Division of Genetics and Physiology; Department of Biology; University of Turku; Turku, Finland
| | - Harri Savilahti
- Division of Genetics and Physiology; Department of Biology; University of Turku; Turku, Finland
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Zhang B, Zhang L, Dai R, Yu M, Zhao G, Ding X. An efficient procedure for marker-free mutagenesis of S. coelicolor by site-specific recombination for secondary metabolite overproduction. PLoS One 2013; 8:e55906. [PMID: 23409083 PMCID: PMC3567011 DOI: 10.1371/journal.pone.0055906] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 01/07/2013] [Indexed: 11/19/2022] Open
Abstract
Streptomyces bacteria are known for producing important natural compounds by secondary metabolism, especially antibiotics with novel biological activities. Functional studies of antibiotic-biosynthesizing gene clusters are generally through homologous genomic recombination by gene-targeting vectors. Here, we present a rapid and efficient method for construction of gene-targeting vectors. This approach is based on Streptomyces phage φBT1 integrase-mediated multisite in vitro site-specific recombination. Four ‘entry clones’ were assembled into a circular plasmid to generate the destination gene-targeting vector by a one-step reaction. The four ‘entry clones’ contained two clones of the upstream and downstream flanks of the target gene, a selectable marker and an E. coli-Streptomyces shuttle vector. After targeted modification of the genome, the selectable markers were removed by φC31 integrase-mediated in vivo site-specific recombination between pre-placed attB and attP sites. Using this method, part of the calcium-dependent antibiotic (CDA) and actinorhodin (Act) biosynthetic gene clusters were deleted, and the rrdA encoding RrdA, a negative regulator of Red production, was also deleted. The final prodiginine production of the engineered strain was over five times that of the wild-type strain. This straightforward φBT1 and φC31 integrase-based strategy provides an alternative approach for rapid gene-targeting vector construction and marker removal in streptomycetes.
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Affiliation(s)
- Bo Zhang
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Lin Zhang
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Key Laboratory of Synthetic biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Ruixue Dai
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Meiying Yu
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Guoping Zhao
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Key Laboratory of Synthetic biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
- Department of Microbiology and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
- * E-mail: (GZ); (XD)
| | - Xiaoming Ding
- Department of Microbiology and Microbial Engineering, School of Life Sciences, Fudan University, Shanghai, China
- * E-mail: (GZ); (XD)
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Heredia NJ, Beer NR, Hara CA, Hiddessen AL, Bailey CG. In vitro double transposition for DNA identification. Anal Biochem 2010; 399:78-83. [DOI: 10.1016/j.ab.2009.11.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Revised: 11/18/2009] [Accepted: 11/19/2009] [Indexed: 11/24/2022]
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Turakainen H, Saarimäki-Vire J, Sinjushina N, Partanen J, Savilahti H. Transposition-based method for the rapid generation of gene-targeting vectors to produce Cre/Flp-modifiable conditional knock-out mice. PLoS One 2009; 4:e4341. [PMID: 19194496 PMCID: PMC2632748 DOI: 10.1371/journal.pone.0004341] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Accepted: 12/24/2008] [Indexed: 11/18/2022] Open
Abstract
Conditional gene targeting strategies are progressively used to study gene function tissue-specifically and/or at a defined time period. Instrumental to all of these strategies is the generation of targeting vectors, and any methodology that would streamline the procedure would be highly beneficial. We describe a comprehensive transposition-based strategy to produce gene-targeting vectors for the generation of mouse conditional alleles. The system employs a universal cloning vector and two custom-designed mini-Mu transposons. It produces targeting constructions directly from BAC clones, and the alleles generated are modifiable by Cre and Flp recombinases. We demonstrate the applicability of the methodology by modifying two mouse genes, Chd22 and Drapc1. This straightforward strategy should be readily suitable for high-throughput targeting vector production.
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Affiliation(s)
- Hilkka Turakainen
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - Jonna Saarimäki-Vire
- Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - Natalia Sinjushina
- Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - Juha Partanen
- Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - Harri Savilahti
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland
- * E-mail:
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Aoyama M, Agari K, Sun-Wada GH, Futai M, Wada Y. Simple and straightforward construction of a mouse gene targeting vector using in vitro transposition reactions. Nucleic Acids Res 2005; 33:e52. [PMID: 15784610 PMCID: PMC1069132 DOI: 10.1093/nar/gni055] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2005] [Revised: 03/07/2005] [Accepted: 03/07/2005] [Indexed: 11/12/2022] Open
Abstract
In a gene targeting experiment, the generation of a targeting construct often requires complex DNA manipulations. We developed a set of cassettes and plasmids useful for creating targeting vectors to modify the mammalian genome. A positive selection marker cassette (PGK/EM7p-npt), which included dual prokaryotic and eukaryotic promoters to permit consecutive selection for recombination in Escherichia coli and then in mouse embryonic stem cells, was flanked by two FRT-loxP sequences. The PGK/EM7p-npt cassette was placed between the minimum regions of a Tn7 transposable element for insertion into another DNA by means of Tn7 transposase in vitro. We also constructed a plasmid having a loxP-Zeo-loxP cassette between the modified Tn5 outer elements. These cassettes can be integrated randomly into a given genomic DNA through the in vitro transposition reaction, thus producing a collection of genomic segments flanked by loxP sites (floxed) at various positions without the use of restriction enzymes and DNA ligase. We confirmed that this system remarkably reduced the time and labor for the construction of complex gene targeting vectors.
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Affiliation(s)
- Minako Aoyama
- Division of Biological Science, Institute for Scientific and Industrial Research, Osaka University and CREST, Japan Science and Technology AgencyMihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
- Futai Special Laboratory, Microbial Chemistry Research Center, Microbial Chemistry Research Foundation and CREST, Japan Science and Technology Agency3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan
| | - Kazuko Agari
- Division of Biological Science, Institute for Scientific and Industrial Research, Osaka University and CREST, Japan Science and Technology AgencyMihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
- Futai Special Laboratory, Microbial Chemistry Research Center, Microbial Chemistry Research Foundation and CREST, Japan Science and Technology Agency3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan
| | - Ge-Hong Sun-Wada
- Division of Biological Science, Institute for Scientific and Industrial Research, Osaka University and CREST, Japan Science and Technology AgencyMihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
- Futai Special Laboratory, Microbial Chemistry Research Center, Microbial Chemistry Research Foundation and CREST, Japan Science and Technology Agency3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan
| | - Masamitsu Futai
- Futai Special Laboratory, Microbial Chemistry Research Center, Microbial Chemistry Research Foundation and CREST, Japan Science and Technology Agency3-14-23 Kamiosaki, Shinagawa-ku, Tokyo 141-0021, Japan
| | - Yoh Wada
- To whom correspondence should be addressed. Tel: +81 6 6879 8481; Fax: +81 6 6875 5724;
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