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Montelongo Hernandez C, Putonti C, Wolfe AJ. Characterizing Plasmids in Bacteria Species Relevant to Urinary Health. Microbiol Spectr 2021; 9:e0094221. [PMID: 34937183 PMCID: PMC8694116 DOI: 10.1128/spectrum.00942-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 11/25/2021] [Indexed: 12/21/2022] Open
Abstract
The urinary tract has a microbial community (the urinary microbiota or urobiota) that has been associated with human health. Whole genome sequencing of bacteria is a powerful tool, allowing investigation of the genomic content of the urobiota, also called the urinary microbiome (urobiome). Bacterial plasmids are a significant component of the urobiome yet are understudied. Because plasmids can be vectors and reservoirs for clinically relevant traits, they are important for urobiota dynamics and thus may have relevance to urinary health. In this project, we sought plasmids in 11 clinically relevant urinary species: Aerococcus urinae, Corynebacterium amycolatum, Enterococcus faecalis, Escherichia coli, Gardnerella vaginalis, Klebsiella pneumoniae, Lactobacillus gasseri, Lactobacillus jensenii, Staphylococcus epidermidis, Streptococcus anginosus, and Streptococcus mitis. We found evidence of plasmids in E. faecalis, E. coli, K. pneumoniae, S. epidermidis, and S. anginosus but insufficient evidence in other species sequenced thus far. Some identified plasmidic assemblies were predicted to have putative virulence and/or antibiotic resistance genes, although the majority of their annotated coding regions were of unknown predicted function. In this study, we report on plasmids from urinary species as a first step to understanding the role of plasmids in the bacterial urobiota. IMPORTANCE The microbial community of the urinary tract (urobiota) has been associated with human health. Whole genome sequencing of bacteria permits examination of urobiota genomes, including plasmids. Because plasmids are vectors and reservoirs for clinically relevant traits, they are important for urobiota dynamics and thus may have relevance to urinary health. Currently, urobiota plasmids are understudied. Here, we sought plasmids in 11 clinically relevant urinary species. We found evidence of plasmids in E. faecalis, E. coli, K. pneumoniae, S. epidermidis, and S. anginosus but insufficient evidence in the other 6 species. We identified putative virulence and/or antibiotic resistance genes in some of the plasmidic assemblies, but most of their annotated coding regions were of unknown function. This is a first step to understanding the role of plasmids in the bacterial urobiota.
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Affiliation(s)
- Cesar Montelongo Hernandez
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
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Liu HW, Hu Y, Ren Y, Nam H, Santos JL, Ng S, Gong L, Brummet M, Carrington CA, Ullman CG, Pomper MG, Minn I, Mao HQ. Scalable Purification of Plasmid DNA Nanoparticles by Tangential Flow Filtration for Systemic Delivery. ACS Appl Mater Interfaces 2021; 13:30326-30336. [PMID: 34162211 PMCID: PMC9701136 DOI: 10.1021/acsami.1c05750] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Plasmid DNA (pDNA) nanoparticles synthesized by complexation with linear polyethylenimine (lPEI) are one of the most effective non-viral gene delivery vehicles. However, the lack of scalable and reproducible production methods and the high toxicity have hindered their clinical translation. Previously, we have developed a scalable flash nanocomplexation (FNC) technique to formulate pDNA/lPEI nanoparticles using a continuous flow process. Here, we report a tangential flow filtration (TFF)-based scalable purification method to reduce the uncomplexed lPEI concentration in the nanoparticle formulation and improve its biocompatibility. The optimized procedures achieved a 60% reduction of the uncomplexed lPEI with preservation of the nanoparticle size and morphology. Both in vitro and in vivo studies showed that the purified nanoparticles significantly reduced toxicity while maintaining transfection efficiency. TFF also allows for gradual exchange of solvents to isotonic solutions and further concentrating the nanoparticles for injection. Combining FNC production and TFF purification, we validated the purified pDNA/lPEI nanoparticles for future clinical translation of this gene nanomedicine.
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Affiliation(s)
- Heng-Wen Liu
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Yizong Hu
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Yong Ren
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Hwanhee Nam
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jose Luis Santos
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Shirley Ng
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Like Gong
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Mary Brummet
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | | | | | - Martin G. Pomper
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Il Minn
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Hai-Quan Mao
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, MD 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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Delfino D, Mori G, Rivetti C, Grigoletto A, Bizzotto G, Cavozzi C, Malatesta M, Cavazzini D, Pasut G, Percudani R. Actin-Resistant DNase1L2 as a Potential Therapeutics for CF Lung Disease. Biomolecules 2021; 11:biom11030410. [PMID: 33802146 PMCID: PMC8002113 DOI: 10.3390/biom11030410] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/02/2021] [Accepted: 03/05/2021] [Indexed: 02/07/2023] Open
Abstract
In cystic fibrosis (CF), the accumulation of viscous lung secretions rich in DNA and actin is a major cause of chronic inflammation and recurrent infections leading to airway obstruction. Mucolytic therapy based on recombinant human DNase1 reduces CF mucus viscosity and promotes airway clearance. However, the marked susceptibility to actin inhibition of this enzyme prompts the research of alternative treatments that could overcome this limitation. Within the human DNase repertoire, DNase1L2 is ideally suited for this purpose because it exhibits metal-dependent endonuclease activity on plasmid DNA in a broad range of pH with acidic optimum and is minimally inhibited by actin. When tested on CF artificial mucus enriched with actin, submicromolar concentrations of DNase1L2 reduces mucus viscosity by 50% in a few seconds. Inspection of superimposed model structures of DNase1 and DNase1L2 highlights differences at the actin-binding interface that justify the increased resistance of DNase1L2 toward actin inhibition. Furthermore, a PEGylated form of the enzyme with preserved enzymatic activity was obtained, showing interesting results in terms of activity. This work represents an effort toward the exploitation of natural DNase variants as promising alternatives to DNase1 for the treatment of CF lung disease.
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Affiliation(s)
- Danila Delfino
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (D.D.); (C.C.); (M.M.); (D.C.); (R.P.)
| | - Giulia Mori
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (D.D.); (C.C.); (M.M.); (D.C.); (R.P.)
- Correspondence: (G.M.); (C.R.); (G.P.)
| | - Claudio Rivetti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (D.D.); (C.C.); (M.M.); (D.C.); (R.P.)
- Correspondence: (G.M.); (C.R.); (G.P.)
| | - Antonella Grigoletto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy; (A.G.); (G.B.)
| | - Gloria Bizzotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy; (A.G.); (G.B.)
| | - Cristian Cavozzi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (D.D.); (C.C.); (M.M.); (D.C.); (R.P.)
| | - Marco Malatesta
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (D.D.); (C.C.); (M.M.); (D.C.); (R.P.)
| | - Davide Cavazzini
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (D.D.); (C.C.); (M.M.); (D.C.); (R.P.)
| | - Gianfranco Pasut
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy; (A.G.); (G.B.)
- Correspondence: (G.M.); (C.R.); (G.P.)
| | - Riccardo Percudani
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy; (D.D.); (C.C.); (M.M.); (D.C.); (R.P.)
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Coelho-Rocha ND, Barroso FAL, Tavares LM, Dos Santos ESS, Azevedo V, Drumond MM, Mancha-Agresti P. Main Features of DNA-Based Vectors for Use in Lactic Acid Bacteria and Update Protocols. Methods Mol Biol 2021; 2197:285-304. [PMID: 32827144 DOI: 10.1007/978-1-0716-0872-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
DNA vaccines have been used as a promising strategy for delivery of immunogenic and immunomodulatory molecules into the host cells. Although, there are some obstacles involving the capability of the plasmid vector to reach the cell nucleus in great number to promote the expected benefits. In order to improve the delivery and, consequently, increase the expression levels of the target proteins carried by DNA vaccines, alternative methodologies have been explored, including the use of non-pathogenic bacteria as delivery vectors to carry, deliver, and protect the DNA from degradation, enhancing plasmid expression.
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Affiliation(s)
- Nina D Coelho-Rocha
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Fernanda A L Barroso
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Laísa M Tavares
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Ester S S Dos Santos
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Vasco Azevedo
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Mariana M Drumond
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Center of Federal Education of Minas Gerais (CEFET-MG), Belo Horizonte, Minas Gerais, Brazil
| | - Pamela Mancha-Agresti
- Laboratory of Cellular and Molecular Genetics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
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Abstract
CRISPR-mediated gene activation (CRISPRa) can be used to target endogenous genes for activation. By targeting pluripotency-associated reprogramming factors, human fibroblasts can be reprogrammed into induced pluripotent stem cells (iPSCs). Here, we describe a method for the derivation of iPSCs from human fibroblasts using episomal plasmids encoding CRISPRa components. This chapter also provides procedure to assemble guide RNA cassettes and generation of multiplexed guide plasmids for readers who want to design their own guide RNAs.
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Affiliation(s)
- Jere Weltner
- Stem Cells and Metabolism Research Program, Biomedicum Stem Cell Center, University of Helsinki, Helsinki, Finland.
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden.
- Division of Obstetrics and Gynecology, Karolinska Universitetssjukhuset, Stockholm, Sweden.
| | - Ras Trokovic
- Stem Cells and Metabolism Research Program, Biomedicum Stem Cell Center, University of Helsinki, Helsinki, Finland.
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6
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Abstract
Purification of high-quality plasmid DNA in large quantities is a crucial step in its production for therapeutic use and is usually conducted by different chromatographic techniques. Large-scale preparations require the optimization of yield and homogeneity, while maximizing removal of contaminants and preserving molecular integrity. The advantages of Convective Interaction Media® (CIM®) monolith stationary phases, including low backpressure, fast separation of macromolecules, and flow-rate-independent resolution qualified them to be used effectively in separation of plasmid DNA on laboratory as well as on large scale. A development and scale-up of plasmid DNA downstream process based on chromatographic monoliths is described and discussed below. Special emphasis is put on the introduction of process analytical technology principles and tools for optimization and control of a downstream process.
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Kang B, Maeshige T, Okamoto A, Kataoka Y, Yamamoto S, Rikiishi K, Tani A, Sawada H, Suzuki K. The Presence of the Hairy-Root-Disease-Inducing (Ri) Plasmid in Wheat Endophytic Rhizobia Explains a Pathogen Reservoir Function of Healthy Resistant Plants. Appl Environ Microbiol 2020; 86:e00671-20. [PMID: 32631868 PMCID: PMC7440801 DOI: 10.1128/aem.00671-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 06/23/2020] [Indexed: 11/20/2022] Open
Abstract
A large number of strains in the Rhizobium radiobacter species complex (biovar 1 Agrobacterium) have been known as causative pathogens for crown gall and hairy root diseases. Strains within this complex were also found as endophytes in many plant species with no symptoms. The aim of this study was to reveal the endophyte variation of this complex and how these endophytic strains differ from pathogenic strains. In this study, we devised a simple but effective screening method by exploiting the high resolution power of mass spectrometry. We screened endophyte isolates from young wheat and barley plants, which are resistant to the diseases, and identified seven isolates from wheat as members of the R. radiobacter species complex. Through further analyses, we assigned five strains to the genomovar (genomic group) G1 and two strains to G7 in R. radiobacter Notably, these two genomovar groups harbor many known pathogenic strains. In fact, the two G7 endophyte strains showed pathogenicity on tobacco, as well as the virulence prerequisites, including a 200-kbp Ri plasmid. All five G1 strains possessed a 500-kbp plasmid, which is present in well-known crown gall pathogens. These data strongly suggest that healthy wheat plants are reservoirs for pathogenic strains of R. radiobacterIMPORTANCE Crown gall and hairy root diseases exhibit very wide host-plant ranges that cover gymnosperm and dicot plants. The Rhizobium radiobacter species complex harbors causative agents of the two diseases. Recently, endophyte isolates from many plant species have been assigned to this species complex. We isolated seven endophyte strains belonging to the species complex from wheat plants and revealed their genomovar affiliations and plasmid profile. The significance of this study is the finding of the genomovar correlation between the endophytes and the known pathogens, the presence of a virulence ability in two of the seven endophyte strains, and the high ratio of the pathogenic strains in the endophyte strains. This study therefore provides convincing evidence that could unravel the mechanism that maintains pathogenic agents of this species and sporadically delivers them to susceptible plants.
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Affiliation(s)
- Byoungwoo Kang
- Basic Biology Program, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
| | - Taichi Maeshige
- Department of Biological Science, Graduate School of Science, Hiroshima University, Hiroshima, Japan
| | - Aya Okamoto
- Department of Biological Science, Graduate School of Science, Hiroshima University, Hiroshima, Japan
| | - Yui Kataoka
- Department of Biological Science, Graduate School of Science, Hiroshima University, Hiroshima, Japan
| | - Shinji Yamamoto
- Department of Biological Science, Graduate School of Science, Hiroshima University, Hiroshima, Japan
| | - Kazuhide Rikiishi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Akio Tani
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Hiroyuki Sawada
- Genetic Resources Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan
| | - Katsunori Suzuki
- Basic Biology Program, Graduate School of Integrated Sciences for Life, Hiroshima University, Hiroshima, Japan
- Department of Biological Science, Graduate School of Science, Hiroshima University, Hiroshima, Japan
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Cazares A, Moore MP, Hall JPJ, Wright LL, Grimes M, Emond-Rhéault JG, Pongchaikul P, Santanirand P, Levesque RC, Fothergill JL, Winstanley C. A megaplasmid family driving dissemination of multidrug resistance in Pseudomonas. Nat Commun 2020; 11:1370. [PMID: 32170080 PMCID: PMC7070040 DOI: 10.1038/s41467-020-15081-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 02/13/2020] [Indexed: 11/10/2022] Open
Abstract
Multidrug resistance (MDR) represents a global threat to health. Here, we used whole genome sequencing to characterise Pseudomonas aeruginosa MDR clinical isolates from a hospital in Thailand. Using long-read sequence data we obtained complete sequences of two closely related megaplasmids (>420 kb) carrying large arrays of antibiotic resistance genes located in discrete, complex and dynamic resistance regions, and revealing evidence of extensive duplication and recombination events. A comprehensive pangenomic and phylogenomic analysis indicates that: 1) these large plasmids comprise an emerging family present in different members of the Pseudomonas genus, and associated with multiple sources (geographical, clinical or environmental); 2) the megaplasmids encode diverse niche-adaptive accessory traits, including multidrug resistance; 3) the accessory genome of the megaplasmid family is highly flexible and diverse. The history of the megaplasmid family, inferred from our analysis of the available database, suggests that members carrying multiple resistance genes date back to at least the 1970s.
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Affiliation(s)
- Adrian Cazares
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
| | - Matthew P Moore
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - James P J Hall
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, UK
| | - Laura L Wright
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Macauley Grimes
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | | | | | | | - Roger C Levesque
- Institute for Integrative and Systems Biology (IBIS), University Laval, Quebec City, QC, Canada
| | - Joanne L Fothergill
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Craig Winstanley
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
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Abstract
Plasmids play a major role in the bacterial adaptation to changing and stressful environmental conditions caused by antibiotics, heavy metals, and disinfectants. However, the investigation of the ecology and diversity of environmental plasmids is challenging due to their typically low abundance in soil bacterial communities and the low cultivability of their hosts. Here we discuss the potentials and limitations of cultivation-dependent and cultivation-independent approaches for detecting and quantifying plasmids in total community DNA from environmental samples. Protocols for PCR-based detection of plasmid-specific sequences in total community DNA are presented. Furthermore, protocols to obtain and characterize plasmids either from isolates (endogenous plasmid isolation) or by capturing into a recipient strain by biparental and triparental mating will be provided.
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Affiliation(s)
- Khald Blau
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Sven Jechalke
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Braunschweig, Germany
| | - Kornelia Smalla
- Institute for Epidemiology and Pathogen Diagnostics, Julius Kühn-Institut (JKI), Federal Research Centre for Cultivated Plants, Braunschweig, Germany.
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Santos T, Pereira P, Queiroz JA, Cruz C, Sousa F. Plasmid production and purification: An integrated experiment-based biochemistry and biotechnology laboratory course. Biochem Mol Biol Educ 2019; 47:638-643. [PMID: 31390150 DOI: 10.1002/bmb.21290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 07/14/2019] [Accepted: 07/19/2019] [Indexed: 06/10/2023]
Abstract
This laboratory experiment describes the production and purification of plasmid DNA for undergraduate biochemistry and biotechnology courses. This experiment performed in a one-week period includes the protocols for plasmid pVAX1-LacZ production in Escherichia coli DH5α cells and subsequent purification of supercoiled pVAX1-LacZ. Firstly, the students use a growth medium that favors the replication of the plasmid resulting in a higher plasmid production during exponential growth. Afterwards, alkaline lysis is done to disrupt the bacterial cells and recover pVAX1-LacZ plasmid. Lastly, they perform the purification of pVAX1-LacZ supercoiled isoform by L-histidine chromatography, followed by agarose gel electrophoresis to characterize the separation of supercoiled isoform from contaminants. The proposed experiment provides an opportunity for students to acquire these skills that are routinely used in biochemistry and biotechnology laboratories. © 2019 International Union of Biochemistry and Molecular Biology, 47(6):638-643, 2019.
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Affiliation(s)
- Tiago Santos
- CICS-UBI-Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - Patrícia Pereira
- CICS-UBI-Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - João A Queiroz
- CICS-UBI-Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - Carla Cruz
- CICS-UBI-Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - Fani Sousa
- CICS-UBI-Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
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11
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Fang Z, Tan J, Wu S, Li M, Xu C, Xie Z, Zhu H. PPR-Meta: a tool for identifying phages and plasmids from metagenomic fragments using deep learning. Gigascience 2019; 8:giz066. [PMID: 31220250 PMCID: PMC6586199 DOI: 10.1093/gigascience/giz066] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 03/26/2019] [Accepted: 05/14/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Phages and plasmids are the major components of mobile genetic elements, and fragments from such elements generally co-exist with chromosome-derived fragments in sequenced metagenomic data. However, there is a lack of efficient methods that can simultaneously identify phages and plasmids in metagenomic data, and the existing tools identifying either phages or plasmids have not yet presented satisfactory performance. FINDINGS We present PPR-Meta, a 3-class classifier that allows simultaneous identification of both phage and plasmid fragments from metagenomic assemblies. PPR-Meta consists of several modules for predicting sequences of different lengths. Using deep learning, a novel network architecture, referred to as the Bi-path Convolutional Neural Network, is designed to improve the performance for short fragments. PPR-Meta demonstrates much better performance than currently available similar tools individually for phage or plasmid identification, while testing on both artificial contigs and real metagenomic data. PPR-Meta is freely available via http://cqb.pku.edu.cn/ZhuLab/PPR_Meta or https://github.com/zhenchengfang/PPR-Meta. CONCLUSIONS To the best of our knowledge, PPR-Meta is the first tool that can simultaneously identify phage and plasmid fragments efficiently and reliably. The software is optimized and can be easily run on a local PC by non-computer professionals. We developed PPR-Meta to promote the research on mobile genetic elements and horizontal gene transfer.
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Affiliation(s)
- Zhencheng Fang
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
- Center for Quantitative Biology, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
| | - Jie Tan
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
- Center for Quantitative Biology, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
| | - Shufang Wu
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
- Center for Quantitative Biology, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
| | - Mo Li
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
- Center for Quantitative Biology, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
- Peking University-Tsinghua University - National Institute of Biological Sciences (PTN) joint PhD program, School of Life Sciences, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
| | - Congmin Xu
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
- Center for Quantitative Biology, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, 631 Cherry St, Atlanta, Georgia 30332, GA, USA
| | - Zhongjie Xie
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
- Center for Quantitative Biology, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
| | - Huaiqiu Zhu
- State Key Laboratory for Turbulence and Complex Systems and Department of Biomedical Engineering, College of Engineering, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
- Center for Quantitative Biology, Peking University, No.5 Yiheyuan Road Haidian District, Beijing 100871, China
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12
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Kilic T, Popov AN, Burk-Körner A, Koromyslova A, zur Hausen H, Bund T, Hansman GS. Structural analysis of a replication protein encoded by a plasmid isolated from a multiple sclerosis patient. Acta Crystallogr D Struct Biol 2019; 75:498-504. [PMID: 31063152 PMCID: PMC6503762 DOI: 10.1107/s2059798319003991] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/23/2019] [Indexed: 12/15/2022] Open
Abstract
Bovine meat and milk factors (BMMFs) are circular, single-stranded episomal DNAs that have been detected in bovine meat and milk products. BMMFs are thought to have roles in human malignant and degenerative diseases. BMMFs encode a replication initiator protein (Rep) that is actively transcribed and translated in human cells. In this study, a Rep WH1 domain encoded on a BMMF (MSBI1.176) isolated from a multiple sclerosis human brain sample was determined to 1.53 Å resolution using X-ray crystallography. The overall structure of the MSBI1.176 WH1 domain was remarkably similar to other Rep structures, despite having a low (28%) amino-acid sequence identity. The MSBI1.176 WH1 domain contained elements common to other Reps, including five α-helices, five β-strands and a hydrophobic pocket. These new findings suggest that the MSBI1.176 Rep might have comparable roles and functions to other known Reps of different origins.
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Affiliation(s)
- Turgay Kilic
- Schaller Research Group at the University of Heidelberg, Heidelberg, Germany
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
| | - Alexander N. Popov
- Structural Biology Group, European Synchrotron Radiation Facility (ESRF), Grenoble, France
| | - Amelie Burk-Körner
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Biosciences Faculty, University of Heidelberg, Heidelberg, Germany
| | - Anna Koromyslova
- Schaller Research Group at the University of Heidelberg, Heidelberg, Germany
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
| | | | - Timo Bund
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Grant S. Hansman
- Schaller Research Group at the University of Heidelberg, Heidelberg, Germany
- Department of Infectious Diseases, Virology, University of Heidelberg, Heidelberg, Germany
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13
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Abstract
Compared to traditional means, modern DNA assembly methods allow cloning of large, multigenic vectors for plant transformation in rapid fashion. These methods are often robust and efficient and can assemble multiple DNA fragments into a single vector in one reaction. Here we describe the use of an automated DNA assembly platform for the generation of complex, multigenic T-DNA binary vectors using a hierarchical Golden Gate cloning strategy. These DNA constructs contained diverse DNA elements for the expression of multiple genes for trait stacking in the crop of interest. This platform streamlines the DNA assembly and validation process through high-efficiency cloning methods, integrated automation equipment, and increased throughput. The implementation of this platform removes bottlenecks for routine molecular biology and opens new possibilities for downstream experimental idea testing.
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Affiliation(s)
- David G J Mann
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Indianapolis, IN, USA.
| | - Scott A Bevan
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Indianapolis, IN, USA
| | - Anthony J Harvey
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Indianapolis, IN, USA
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14
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Jain P, Sudhanthirakodi S, Chowdhury G, Joshi S, Anandan S, Ray U, Mukhopadhyay A, Dutta S. Antimicrobial resistance, plasmid, virulence, multilocus sequence typing and pulsed-field gel electrophoresis profiles of Salmonella enterica serovar Typhimurium clinical and environmental isolates from India. PLoS One 2018; 13:e0207954. [PMID: 30540810 PMCID: PMC6291080 DOI: 10.1371/journal.pone.0207954] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 11/08/2018] [Indexed: 01/19/2023] Open
Abstract
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a common serovar associated with non-typhoidal salmonellosis globally. However, there is insufficient data on molecular characterization of S. Typhimurium isolates from India. This study was undertaken to determine the antimicrobial resistance (AMR), plasmid, virulence profiles and molecular subtypes of S. Typhimurium Indian isolates (n = 70) of clinical and environmental origin isolated during 2010–2017. Antimicrobial susceptibility and minimum inhibitory concentrations were determined by disc diffusion and E-test methods respectively. Plasmid extraction was done following standard protocol. AMR genes, virulence genes and plasmid incompatibility types were detected by PCR; Pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST) were used for molecular subtyping. Majority (57%) of the study isolates was pan susceptible; five AMR profiles were observed among the resistant (43%) isolates. AMR was significantly (p = 0.004) associated with extra-intestinal isolates than intestinal isolates.The class 1 integron and plasmid-mediated quinolone resistance genes (qnrB1, qnrS1) in the resistant isolates were transferable by conjugation. Plasmids (≥1) ranging from 1.9 to 254kb size and of IncFIIS and/or FIB type were found in most isolates. A total of 39 pulsotypes by PFGE and four sequence types by MLST like ST36 (55.7%), ST19 (32.9%), ST313 (10%) and ST213 (1.4%) were observed. ST36 and ST19 were found circulating in both clinical and environmental host, while ST313 isolates had an exclusive clinical origin. All ST19 isolates (100%) were drug-resistant, while isolates belonging to ST313 (100%), ST213 (100%) and ST36 (82%) were pan susceptible. The virulence plasmid (VP) genes (spvB- spvC) were present in all genotypes except ST36. The VP was significantly (p<0.001) associated with extra-intestinal than intestinal isolates. Some environmental and clinical isolates were clonal indicating their zoonotic transmission. Knowledge on the molecular subtypes and AMR profiles of locally prevalent Salmonella serotypes is important for effective control of spread of resistant organisms. The MLST of S. Typhimurium isolates and its association with AMR, virulence profiles was not reported earlier from India.
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Affiliation(s)
- Priyanka Jain
- Division of Bacteriology, Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | | | - Goutam Chowdhury
- Division of Bacteriology, Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Sangeeta Joshi
- Hospital Infection Control, Manipal Hospital, Bangalore, Karnataka, India
| | - Shalini Anandan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Ujjwayni Ray
- Department of Microbiology, Apollo Gleneagles Hospitals, Kolkata, West Bengal, India
| | - Asish Mukhopadhyay
- Division of Bacteriology, Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Shanta Dutta
- Division of Bacteriology, Indian Council of Medical Research-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
- * E-mail:
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15
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Heine T, Zimmerling J, Ballmann A, Kleeberg SB, Rückert C, Busche T, Winkler A, Kalinowski J, Poetsch A, Scholtissek A, Oelschlägel M, Schmidt G, Tischler D. On the Enigma of Glutathione-Dependent Styrene Degradation in Gordonia rubripertincta CWB2. Appl Environ Microbiol 2018; 84:e00154-18. [PMID: 29475871 PMCID: PMC5930330 DOI: 10.1128/aem.00154-18] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 02/19/2018] [Indexed: 02/05/2023] Open
Abstract
Among bacteria, only a single styrene-specific degradation pathway has been reported so far. It comprises the activity of styrene monooxygenase, styrene oxide isomerase, and phenylacetaldehyde dehydrogenase, yielding phenylacetic acid as the central metabolite. The alternative route comprises ring-hydroxylating enzymes and yields vinyl catechol as central metabolite, which undergoes meta-cleavage. This was reported to be unspecific and also allows the degradation of benzene derivatives. However, some bacteria had been described to degrade styrene but do not employ one of those routes or only parts of them. Here, we describe a novel "hybrid" degradation pathway for styrene located on a plasmid of foreign origin. As putatively also unspecific, it allows metabolizing chemically analogous compounds (e.g., halogenated and/or alkylated styrene derivatives). Gordonia rubripertincta CWB2 was isolated with styrene as the sole source of carbon and energy. It employs an assembled route of the styrene side-chain degradation and isoprene degradation pathways that also funnels into phenylacetic acid as the central metabolite. Metabolites, enzyme activity, genome, transcriptome, and proteome data reinforce this observation and allow us to understand this biotechnologically relevant pathway, which can be used for the production of ibuprofen.IMPORTANCE The degradation of xenobiotics by bacteria is not only important for bioremediation but also because the involved enzymes are potential catalysts in biotechnological applications. This study reveals a novel degradation pathway for the hazardous organic compound styrene in Gordonia rubripertincta CWB2. This study provides an impressive illustration of horizontal gene transfer, which enables novel metabolic capabilities. This study presents glutathione-dependent styrene metabolization in an (actino-)bacterium. Further, the genomic background of the ability of strain CWB2 to produce ibuprofen is demonstrated.
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Affiliation(s)
- Thomas Heine
- Institute of Biosciences, TU Bergakademie Freiberg, Freiberg, Germany
| | | | - Anne Ballmann
- Institute of Biosciences, TU Bergakademie Freiberg, Freiberg, Germany
| | | | - Christian Rückert
- Technologieplattform Genomik, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Tobias Busche
- Technologieplattform Genomik, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Anika Winkler
- Technologieplattform Genomik, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Jörn Kalinowski
- Technologieplattform Genomik, Centrum für Biotechnologie (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Ansgar Poetsch
- Plant Biochemistry, Ruhr University Bochum, Bochum, Germany
- School of Biomedical and Healthcare Sciences, Plymouth University, Plymouth, United Kingdom
| | - Anika Scholtissek
- Institute of Biosciences, TU Bergakademie Freiberg, Freiberg, Germany
| | | | - Gert Schmidt
- Institut für Keramik, Glas- und Baustofftechnik, TU Bergakademie Freiberg, Freiberg, Germany
| | - Dirk Tischler
- Institute of Biosciences, TU Bergakademie Freiberg, Freiberg, Germany
- Microbial Biotechnology, Ruhr University Bochum, Bochum, Germany
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Abdulrahman A, Ghanem A. Recent advances in chromatographic purification of plasmid DNA for gene therapy and DNA vaccines: A review. Anal Chim Acta 2018; 1025:41-57. [PMID: 29801607 DOI: 10.1016/j.aca.2018.04.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 04/03/2018] [Accepted: 04/05/2018] [Indexed: 12/16/2022]
Abstract
The wide spread of infectious diseases have provoked the scientists to develop new types of vaccines. Among the different types of vaccines, the recently discovered plasmid DNA vaccines, have gained tremendous attentions in the last few decades as a modern approach of vaccination. The scientific interest in plasmid DNA vaccines is attributed to their prominent efficacy as they trigger not only the cellular immune response but also the humoral immune responses. Moreover, pDNA vaccines are easily to be stored, shipped and produced. However, the purification of the pDNA vaccines is a crucial step in their production and administration, which is usually conducted by different chromatographic techniques. This review summarizes the most recent chromatographic purification methods provided in the literature during the last five years following our last review in 2013, including affinity chromatography, hydrophobic interaction chromatography, ion exchange chromatography, multimodal chromatography, sample displacement chromatography and miscellaneous chromatographic methods.
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Affiliation(s)
- Ahmed Abdulrahman
- Chirality Program, Faculty of Science and Technology, University of Canberra, Australian Capital Territory (ACT), 2617, Australia
| | - Ashraf Ghanem
- Chirality Program, Faculty of Science and Technology, University of Canberra, Australian Capital Territory (ACT), 2617, Australia. http://www.chiralitygroup.com
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17
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Abstract
Increasingly rich metadata are now being linked to samples that have been whole-genome sequenced. However, much of this information is ignored. This is because linking this metadata to genes, or regions of the genome, usually relies on knowing the gene sequence(s) responsible for the particular trait being measured and looking for its presence or absence in that genome. Examples of this would be the spread of antimicrobial resistance genes carried on mobile genetic elements (MGEs). However, although it is possible to routinely identify the resistance gene, identifying the unknown MGE upon which it is carried can be much more difficult if the starting point is short-read whole-genome sequence data. The reason for this is that MGEs are often full of repeats and so assemble poorly, leading to fragmented consensus sequences. Since mobile DNA, which can carry many clinically and ecologically important genes, has a different evolutionary history from the host, its distribution across the host population will, by definition, be independent of the host phylogeny. It is possible to use this phenomenon in a genome-wide association study to identify both the genes associated with the specific trait and also the DNA linked to that gene, for example the flanking sequence of the plasmid vector on which it is encoded, which follows the same patterns of distribution as the marker gene/sequence itself. We present PlasmidTron, which utilizes the phenotypic data normally available in bacterial population studies, such as antibiograms, virulence factors, or geographical information, to identify traits that are likely to be present on DNA that can randomly reassort across defined bacterial populations. It is also possible to use this methodology to associate unknown genes/sequences (e.g. plasmid backbones) with a specific molecular signature or marker (e.g. resistance gene presence or absence) using PlasmidTron. PlasmidTron uses a k-mer-based approach to identify reads associated with a phylogenetically unlinked phenotype. These reads are then assembled de novo to produce contigs in a fast and scalable-to-large manner. PlasmidTron is written in Python 3 and is available under the open source licence GNU GPL3 from https://github.com/sanger-pathogens/plasmidtron.
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Affiliation(s)
- Andrew J. Page
- Infection Genomics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Present address: Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- *Correspondence: Andrew J. Page,
| | - Alexander Wailan
- Infection Genomics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Yan Shao
- Infection Genomics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Kim Judge
- Infection Genomics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Gordon Dougan
- Infection Genomics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Elizabeth J. Klemm
- Infection Genomics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Nicholas R. Thomson
- Infection Genomics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- London School of Hygiene and Tropical Medicine, London, UK
| | - Jacqueline A. Keane
- Infection Genomics, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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18
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Bertero A, Yiangou L, Brown S, Ortmann D, Pawlowski M, Vallier L. Conditional Manipulation of Gene Function in Human Cells with Optimized Inducible shRNA. ACTA ACUST UNITED AC 2018; 44:5C.4.1-5C.4.48. [PMID: 29512130 DOI: 10.1002/cpsc.45] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The difficulties involved in conditionally perturbing complex gene expression networks represent major challenges toward defining the mechanisms controlling human development, physiology, and disease. We developed an OPTimized inducible KnockDown (OPTiKD) platform that addresses the limitations of previous approaches by allowing streamlined, tightly-controlled, and potent loss-of-function experiments for both single and multiple genes. The method relies on single-step genetic engineering of the AAVS1 genomic safe harbor with an optimized tetracycline-responsive cassette driving one or more inducible short hairpin RNAs (shRNAs). OPTiKD provides homogeneous, dose-responsive, and reversible gene knockdown. When implemented in human pluripotent stem cells (hPSCs), the approach can be then applied to a broad range of hPSC-derived mature cell lineages that include neurons, cardiomyocytes, and hepatocytes. Generation of OPTiKD hPSCs in commonly used culture conditions is simple (plasmid based), rapid (two weeks), and highly efficient (>95%). Overall, this method facilitates the functional annotation of the human genome in health and disease. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
- Alessandro Bertero
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, United Kingdom
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
- Department of Pathology, University of Washington, Seattle, Washington
| | - Loukia Yiangou
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, United Kingdom
- Division of Cardiovascular Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Stephanie Brown
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, United Kingdom
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
| | - Daniel Ortmann
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, United Kingdom
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
| | - Matthias Pawlowski
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, United Kingdom
- Department of Clinical Neuroscience, University of Cambridge, Cambridge, United Kingdom
| | - Ludovic Vallier
- Wellcome Trust-MRC Stem Cell Institute, Anne McLaren Laboratory, University of Cambridge, Cambridge, United Kingdom
- Department of Surgery, University of Cambridge, Cambridge, United Kingdom
- Wellcome Trust Sanger Institute, Hinxton, United Kingdom
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19
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Bryan LK, Alexander ER, Lawhon SD, Cohen ND. Detection of vapN in Rhodococcus equi isolates cultured from humans. PLoS One 2018; 13:e0190829. [PMID: 29300774 PMCID: PMC5754133 DOI: 10.1371/journal.pone.0190829] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 12/20/2017] [Indexed: 11/18/2022] Open
Abstract
Rhodococcus equi can cause severe infections in people, particularly in immunocompromised individuals. The R. equi virulence plasmids (vap) encoding vapA and vapB are linked to development of infections in domestic animals. Recently, a novel virulence plasmid, vapN, was identified in isolates cultured from cattle, but its prevalence or significance in human R. equi infections has not been extensively studied. To determine the prevalence of vapN in a diverse collection of human-derived isolates from different countries, 65 R. equi isolates collected by various institutions from 1984 to 2002 were screened for the presence of vapN and other virulence plasmids through polymerase chain reaction (PCR) using redesigned primer sets. Of the isolates that carried plasmids, 43% (16/37) were vapN-positive and fewer were vapB or vapA-positive (30 and 16%, respectively). This is the first report of vapN carriage in R. equi isolated from human infections. One isolate (H-30) carried vapN but did not amplify the conjugal plasmid transfer gene traA associated with carriage of vap, which could be explained by sequence variation within the traA gene. Another isolate (H-55) amplified traA, but did not amplify vapA, B, or N (traA+vapABN-) with previously described primer sets or those developed for this study. The H-55 traA sequence had 98% identity to traA sequences in vapA plasmids, which suggests that it may carry a variant of previously characterized virulence plasmids or a novel virulence plasmid. Carriage of vapN in R. equi isolates derived from people is not uncommon and more research is needed to determine its significance in the epidemiology and pathogenesis of human R. equi infections.
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Affiliation(s)
- Laura K. Bryan
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
| | - Ellen Ruth Alexander
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Sara D. Lawhon
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Noah D. Cohen
- Department of Large Animal Clinical Sciences, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, United States of America
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20
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Green MR, Sambrook J. Preparation of Plasmid DNA by Alkaline Lysis with Sodium Dodecyl Sulfate: Maxipreps. Cold Spring Harb Protoc 2018; 2018:2018/1/pdb.prot093351. [PMID: 29295898 DOI: 10.1101/pdb.prot093351] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In recent years, with the advent of polymerase chain reaction and the development of highly efficient methods of cloning and DNA sequencing, the need to prepare large quantities of plasmid vectors and recombinants has greatly diminished. In consequence, this protocol, at one time in common use, has been largely replaced by faster and easier column-based purification methods. In this protocol, plasmid DNA is purified from the cleared bacterial lysate by centrifugation to equilibrium in CsCl gradients containing ethidium bromide. These gradients have an aesthetic quality that justifies the continued presentation of a protocol that in many other respects is an antique. The typical yield of high-copy-number plasmid vectors or of amplified low-copy-number vectors prepared by this method is ∼3-5 µg of DNA/mL of original bacterial culture. The yield of recombinant plasmids containing inserts of foreign DNA is usually slightly lower, depending on the size and nature of the cloned DNA fragment.
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21
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Mavrici D, Yambao JC, Lee BG, Quiñones B, He X. Screening for the presence of mcr-1/mcr-2 genes in Shiga toxin-producing Escherichia coli recovered from a major produce-production region in California. PLoS One 2017; 12:e0187827. [PMID: 29117270 PMCID: PMC5678862 DOI: 10.1371/journal.pone.0187827] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 10/26/2017] [Indexed: 12/24/2022] Open
Abstract
The rapid spreading of polymyxin E (colistin) resistance among bacterial strains through the horizontally transmissible mcr-1 and mcr-2 plasmids has become a serious concern. The emergence of these genes in Shiga toxin-producing Escherichia coli (STEC), a group of human pathogenic bacteria was even more worrisome, urging us to investigate the prevalence of mcr genes among STEC isolates. A total of 1000 STEC isolates, recovered from livestock, wildlife, produce and other environmental sources in a major production region for leafy vegetables in California during 2006-2014, were screened by PCR for the presence of plasmid-borne mcr-1 and mcr-2. All isolates tested yielded negative results, indicating if any, the occurrence rate of mcr-1/mcr-2 among STEC was very low in this agricultural region. This study provides valuable information such as sample size needed and methodologies for future surveillance programs of antimicrobial resistance.
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Affiliation(s)
- Daniela Mavrici
- Foodborne Toxin Detection and Prevention Research Unit, Western Regional Research Center, Agriculture Research Service, U.S. Department of Agriculture, Albany, California, United States of America
| | - Jaszemyn C. Yambao
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agriculture Research Service, U.S. Department of Agriculture, Albany, California, United States of America
| | - Bertram G. Lee
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agriculture Research Service, U.S. Department of Agriculture, Albany, California, United States of America
| | - Beatriz Quiñones
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agriculture Research Service, U.S. Department of Agriculture, Albany, California, United States of America
- * E-mail: (XH); (BQ)
| | - Xiaohua He
- Foodborne Toxin Detection and Prevention Research Unit, Western Regional Research Center, Agriculture Research Service, U.S. Department of Agriculture, Albany, California, United States of America
- * E-mail: (XH); (BQ)
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22
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Abstract
This protocol describes the preparation of plasmid DNA from bacterial cultures or from archived cultures, based on the standard miniprep method. The resulting DNA is suitable in quantity and quality for use as template in capillary DNA sequencing. The protocol relies on the use of the Biomek automated liquid handling system.
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23
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Rowley PA. The frenemies within: viruses, retrotransposons and plasmids that naturally infect Saccharomyces yeasts. Yeast 2017; 34:279-292. [PMID: 28387035 DOI: 10.1002/yea.3234] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/28/2017] [Accepted: 03/29/2017] [Indexed: 11/07/2022] Open
Abstract
Viruses are a major focus of current research efforts because of their detrimental impact on humanity and their ubiquity within the environment. Bacteriophages have long been used to study host-virus interactions within microbes, but it is often forgotten that the single-celled eukaryote Saccharomyces cerevisiae and related species are infected with double-stranded RNA viruses, single-stranded RNA viruses, LTR-retrotransposons and double-stranded DNA plasmids. These intracellular nucleic acid elements have some similarities to higher eukaryotic viruses, i.e. yeast retrotransposons have an analogous lifecycle to retroviruses, the particle structure of yeast totiviruses resembles the capsid of reoviruses and segregation of yeast plasmids is analogous to segregation strategies used by viral episomes. The powerful experimental tools available to study the genetics, cell biology and evolution of S. cerevisiae are well suited to further our understanding of how cellular processes are hijacked by eukaryotic viruses, retrotransposons and plasmids. This article has been written to briefly introduce viruses, retrotransposons and plasmids that infect Saccharomyces yeasts, emphasize some important cellular proteins and machineries with which they interact, and suggest the evolutionary consequences of these interactions. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Paul A Rowley
- Department of Biological Sciences, The University of Idaho, Moscow, Idaho, USA
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24
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Baron S, Bardet L, Dubourg G, Fichaux M, Rolain JM. mcr-1 plasmid-mediated colistin resistance gene detection in an Enterobacter cloacae clinical isolate in France. J Glob Antimicrob Resist 2017; 10:35-36. [PMID: 28576739 DOI: 10.1016/j.jgar.2017.05.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 05/01/2017] [Accepted: 05/03/2017] [Indexed: 11/19/2022] Open
Affiliation(s)
- Sophie Baron
- Aix-Marseille Université, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, 27 boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Lucie Bardet
- Aix-Marseille Université, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, 27 boulevard Jean Moulin, 13385 Marseille Cedex 05, France
| | - Gregory Dubourg
- Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, IHU Méditerranée Infection, 264 rue Saint-Pierre, 13385 Marseille Cedex 05, France
| | - Marie Fichaux
- Pôle Oncologie, Spécialités médicales et chirurgicales, Oncologie Médicale et Soins Palliatifs, Centre Hospitalo-Universitaire Timone, IHU Méditerranée Infection, 264 rue Saint-Pierre, 13385 Marseille Cedex 05, France
| | - Jean-Marc Rolain
- Aix-Marseille Université, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, IHU Méditerranée Infection, Facultés de Médecine et de Pharmacie, 27 boulevard Jean Moulin, 13385 Marseille Cedex 05, France.
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Tang M, Loo J, Wang Y, Zhang X, Kwok HC, Hui M, Leung CCH, Kong SK, Wang G, Ho HP. Motor-assisted chip-in-a-tube (MACT): a new 2- and 3-dimensional centrifugal microfluidic platform for biomedical applications. Lab Chip 2017; 17:474-483. [PMID: 28009878 DOI: 10.1039/c6lc01169a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Currently, centrifuge apparatus is primarily an end-point sample processing piece of equipment. The lack of real-time active control has imposed an inherent limitation such that many delicate sample processing steps requiring immediate and accurate intervention have never been possible. We report herein a motor-assisted chip-in-a-tube (MACT) platform in which a microfluidic chip placed inside a common centrifuge canister can be rotated through wireless control in order to manipulate the centrifugal force vector in a 3-dimensional (3D) manner. As a demonstration experiment, we have used our MACT prototype to perform the operation for two common biomedical procedures, namely human blood plasma separation and E. coli plasmid DNA extraction. This simple, yet highly effective and versatile approach may serve as a generic one-for-all platform for a wide range of common laboratory experiments and bioassay applications.
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Affiliation(s)
- Minghui Tang
- Department of Electronic Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Jacky Loo
- Department of Electronic Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Yuye Wang
- Institute of Optical Communication Engineering, Nanjing University, Jiangsu 210009, China.
| | - Xuping Zhang
- Institute of Optical Communication Engineering, Nanjing University, Jiangsu 210009, China.
| | - Ho-Chin Kwok
- Department of Electronic Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
| | - Mamie Hui
- Department of Microbiology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Czarina Chi-Hung Leung
- Department of Anaesthesia and Intensive Care, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Siu-Kai Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Guanghui Wang
- Institute of Optical Communication Engineering, Nanjing University, Jiangsu 210009, China.
| | - Ho-Pui Ho
- Department of Electronic Engineering, The Chinese University of Hong Kong, Shatin, Hong Kong, China.
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26
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Abstract
We describe a one-liter transfection of suspension-adapted Chinese hamster ovary (CHO-DG44) cells using polyethyleneimine (PEI) for DNA delivery. The method involves transfection at a high cell density (5 × 106 cells/mL) by direct addition of plasmid DNA (pDNA) and PEI to the culture and subsequent incubation at 31 °C with agitation by orbital shaking. We also describe an alternative method in which 90% of the pDNA is replaced by nonspecific (filler) DNA, and the production phase is performed at 31 °C in the presence of 0.25% N, N-dimethylacetamide (DMA).
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Affiliation(s)
- Yashas Rajendra
- Laboratory of Cellular Biotechnology (LBTC), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | - Sowmya Balasubramanian
- Laboratory of Cellular Biotechnology (LBTC), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - David L Hacker
- Laboratory of Cellular Biotechnology (LBTC), École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
- Protein Expression Core Facility (PECF), École Polytechnique Fédérale de Lausanne (EPFL), EPFL SV PTECH PTEP, CH B1 423, Station 6, CH-1015, Lausanne, Switzerland.
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Siitonen V, Räty K, Metsä-Ketelä M. Laboratory course on Streptomyces genetics and secondary metabolism. Biochem Mol Biol Educ 2016; 44:492-499. [PMID: 27192442 DOI: 10.1002/bmb.20970] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 02/21/2016] [Indexed: 06/05/2023]
Abstract
The "Streptomyces genetics and secondary metabolism" laboratory course gives an introduction to the versatile soil dwelling Gram-positive bacteria Streptomyces and their secondary metabolism. The course combines genetic modification of Streptomyces; growing of the strain and protoplast preparation, plasmid isolation by alkaline lysis and phenol precipitation, digestions, and ligations prior to protoplast transformation, as well as investigating the secondary metabolites produced by the strains. Thus, the course is a combination of microbiology, molecular biology, and chemistry. After the course the students should understand the relationship between genes, proteins, and the produced metabolites. © 2016 by The International Union of Biochemistry and Molecular Biology, 44(5):492-499, 2016.
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Affiliation(s)
- Vilja Siitonen
- Department of Biochemistry, University of Turku, Turku, FIN-20014, Finland.
| | - Kaj Räty
- Department of Biochemistry, University of Turku, Turku, FIN-20014, Finland
| | - Mikko Metsä-Ketelä
- Department of Biochemistry, University of Turku, Turku, FIN-20014, Finland
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28
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Abstract
Plasmid purification is a basic tool of molecular biologists. Although the development of plasmid isolation kits utilizing silica spin columns reduced the time and labor spent on plasmid purification, achieving large plasmid DNA yields still requires significant time and effort. Here we introduce the Miraprep, a rapid protocol that allows isolation of plasmid DNA using commercial Miniprep kits, but with DNA yields comparable to commercial Maxiprep plasmid purifications. Combining ethanol precipitation with spin column purification, we created a DNA isolation protocol that yields highly concentrated plasmid DNA samples in less than 30 minutes. We show that Miraprep isolated plasmids are as stable as plasmids isolated by standard procedures, can be used for standard molecular biology procedures including DNA sequencing, and can be efficiently transfected into mammalian cells. This new plasmid DNA isolation protocol will significantly reduce time and labor without increasing costs.
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Affiliation(s)
- Mira I. Pronobis
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
| | - Natalie Deuitch
- Department of Biology, University of North Carolina at Chapel Hill, CB#3280, Chapel Hill, NC, United States of America
| | - Mark Peifer
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America
- Department of Biology, University of North Carolina at Chapel Hill, CB#3280, Chapel Hill, NC, United States of America
- * E-mail:
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29
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Nicholson BA, West AC, Mangiamele P, Barbieri N, Wannemuehler Y, Nolan LK, Logue CM, Li G. Genetic Characterization of ExPEC-Like Virulence Plasmids among a Subset of NMEC. PLoS One 2016; 11:e0147757. [PMID: 26800268 PMCID: PMC4723317 DOI: 10.1371/journal.pone.0147757] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 01/07/2016] [Indexed: 12/29/2022] Open
Abstract
Neonatal Meningitis Escherichia coli (NMEC) is one of the most common causes of neonatal bacterial meningitis in the US and elsewhere resulting in mortality or neurologic deficits in survivors. Large plasmids have been shown experimentally to increase the virulence of NMEC in the rat model of neonatal meningitis. Here, 9 ExPEC-like plasmids were isolated from NMEC and sequenced to identify the core and accessory plasmid genes of ExPEC-like virulence plasmids in NMEC and create an expanded plasmid phylogeny. Results showed sequenced virulence plasmids carry a strongly conserved core of genes with predicted functions in five distinct categories including: virulence, metabolism, plasmid stability, mobile elements, and unknown genes. The major functions of virulence-associated and plasmid core genes serve to increase in vivo fitness by adding multiple iron uptake systems to the genetic repertoire to facilitate NMEC’s survival in the host’s low iron environment, and systems to enhance bacterial resistance to host innate immunity. Phylogenetic analysis based on these core plasmid genes showed that at least two lineages of ExPEC-like plasmids could be discerned. Further, virulence plasmids from Avian Pathogenic E. coli and NMEC plasmids could not be differentiated based solely on the genes of the core plasmid genome.
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Affiliation(s)
- Bryon A. Nicholson
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Aaron C. West
- Department of Chemistry, College of Liberal Arts and Sciences, Iowa State University, Ames, Iowa, United States of America
| | - Paul Mangiamele
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Nicolle Barbieri
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Yvonne Wannemuehler
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Lisa K. Nolan
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Catherine M. Logue
- Department of Veterinary Microbiology and Preventive Medicine, College of Veterinary Medicine, Iowa State University, Ames, Iowa, United States of America
| | - Ganwu Li
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, 1802 University Blvd, Iowa State University, Ames, Iowa, 50011, United States of America
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, P. R. China
- * E-mail:
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30
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Carneiro LC, Mendes PVC, Silva SP, Souza GRL, Bataus LAM. Characterization of a Cryptic and Intriguing Low Molecular Weight Plasmid. Curr Microbiol 2015; 72:351-6. [PMID: 26670037 DOI: 10.1007/s00284-015-0959-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 10/24/2015] [Indexed: 11/27/2022]
Abstract
The complete nucleotide sequence of cryptic plasmid pVCM04 isolated from Salmonella enterica serovar Enteritidis was determined and analyzed. pVCM04 contains 3853 bp with 53.6 % GC content and has twelve ORFs with more than 50 amino acids. Five of these sequences showed homology with replication and mobilization proteins. ORF1 and ORF2 showed homology with replication proteins, while ORFs 3-5 showed homology with mobilization proteins. The pVCM04 possesses a region associated with the theta-type replication mechanism. BLASTn search analysis revealed unexpectedly no similarity with sequences deposited in GenBank. The nucleotide sequence of pVCM04 can be divided into two arms: the region between nucleotides 552-1774 (encoding RepA and RepB) and the region between nucleotides 1775-3853 (encoding MobA, MobB and MobC). Codon bias pattern is distinct between mobA and repA, so the program Modeltest was used to select the best evolutionary model to study these genes. The result of ModelTest (model GTR+G for mobA and model HKY+G for repA) suggests that these genes would be subject to different selective pressures. Considering the differences in the codon usage, the selection of two different evolutionary models, and the absence of plasmids with homology to pVCM04 in GenBank, we believe that pVCM04 is a chimeric molecule and represents a new plasmid lineage.
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Affiliation(s)
- Lilian C Carneiro
- Department of Biochemistry and Molecular Biology, Federal University of Goiás, Campus Samambaia, Goiânia, GO, Brazil
| | - Paulo Vinicius C Mendes
- Department of Biochemistry and Molecular Biology, Federal University of Goiás, Campus Samambaia, Goiânia, GO, Brazil
| | - Silvana P Silva
- Department of Biochemistry and Molecular Biology, Federal University of Goiás, Campus Samambaia, Goiânia, GO, Brazil
| | - Guilherme R L Souza
- Department of Biochemistry and Molecular Biology, Federal University of Goiás, Campus Samambaia, Goiânia, GO, Brazil
| | - Luiz Artur M Bataus
- Department of Biochemistry and Molecular Biology, Federal University of Goiás, Campus Samambaia, Goiânia, GO, Brazil.
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Niu XN, Wei ZQ, Zou HF, Xie GG, Wu F, Li KJ, Jiang W, Tang JL, He YQ. Complete sequence and detailed analysis of the first indigenous plasmid from Xanthomonas oryzae pv. oryzicola. BMC Microbiol 2015; 15:233. [PMID: 26498126 PMCID: PMC4619425 DOI: 10.1186/s12866-015-0562-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 10/08/2015] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Bacterial plasmids have a major impact on metabolic function and adaptation of their hosts. An indigenous plasmid was identified in a Chinese isolate (GX01) of the invasive phytopathogen Xanthomonas oryzae pv. oryzicola (Xoc), the causal agent of rice bacterial leaf streak (BLS). To elucidate the biological functions of the plasmid, we have sequenced and comprehensively annotated the plasmid. METHODS The plasmid DNA was extracted from Xoc strain GX01 by alkaline lysis and digested with restriction enzymes. The cloned and subcloned DNA fragments in pUC19 were sequenced by Sanger sequencing. Sequences were assembled by using Sequencher software. Gaps were closed by primer walking and sequencing, and multi-PCRs were conducted through the whole plasmid sequence for verification. BLAST, phylogenetic analysis and dinucleotide calculation were performed for gene annotation and DNA structure analysis. Transformation, transconjugation and stress tolerance tests were carried out for plasmid function assays. RESULTS The indigenous plasmid from Xoc strain GX01, designated pXOCgx01, is 53,206-bp long and has been annotated to possess 64 open reading frames (ORFs), including genes encoding type IV secretion system, heavy metal exporter, plasmid stability factors, and DNA mobile factors, i.e., the Tn3-like transposon. Bioinformatics analysis showed that pXOCgx01 has a mosaic structure containing different genome contexts with distinct genomic heterogeneities. Phylogenetic analysis indicated that the closest relative of pXOCgx01 is pXAC64 from Xanthomonas axonopodis pv. citri str. 306. It was estimated that there are four copies of pXOCgx01 per cell of Xoc GX01 by PCR assay and the calculation of whole genome shotgun sequencing data. We demonstrate that pXOCgx01 is a self-transmissible plasmid and can replicate in some Xanthomonas spp. strains, but not in Escherichia coli DH5α. It could significantly enhance the tolerance of Xanthomonas oryzae pv. oryzae PXO99A to the stresses of heavy metal ions. The plasmid survey indicated that nine out of 257 Xoc Chinese isolates contain plasmids. CONCLUSIONS pXOCgx01 is the first report of indigenous plasmid from Xanthomonas oryzae pv. oryzicola, and the first completely sequenced plasmid from Xanthomonas oryzae species. It is a self-transmissible plasmid and has a mosaic structure, containing genes for macromolecule secretion, heavy metal exportation, and DNA mobile factors, especially the Tn3-like transposon which may provide transposition function for mobile insertion cassette and play a major role in the spread of pathogenicity determinants. The results will be helpful to elucidate the biological significance of this cryptic plasmid and the adaptive evolution of Xoc.
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Affiliation(s)
- Xiang-Na Niu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China.
| | - Zhi-Qiong Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China.
| | - Hai-Fan Zou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China.
| | - Gui-Gang Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China.
| | - Feng Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China.
| | - Kang-Jia Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China.
| | - Wei Jiang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China.
| | - Ji-Liang Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China.
| | - Yong-Qiang He
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, The Key Laboratory of Ministry of Education for Microbial and Plant Genetic Engineering, and College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, 530004, China.
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Huang YM, Zhong LL, Zhang XF, Hu HT, Li YQ, Yang XR, Feng LQ, Huang X, Tian GB. NDM-1-Producing Citrobacter freundii, Escherichia coli, and Acinetobacter baumannii Identified from a Single Patient in China. Antimicrob Agents Chemother 2015; 59:5073-7. [PMID: 26055374 PMCID: PMC4505197 DOI: 10.1128/aac.04682-14] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Accepted: 05/31/2015] [Indexed: 12/15/2022] Open
Abstract
We identified New Delhi metallo-β-lactamase (NDM-1)-producing Citrobacter freundii GB032, Escherichia coli GB102, and Acinetobacter baumannii GB661 in urine and stool samples from a single patient in China. Plasmid profiling and Southern blotting indicated that blaNDM-1 from GB032 and that from GB102 were likely located on the same plasmid, while blaNDM-1 from GB661 was located on a very large (>400-kb) plasmid. This case underscores the broad host range of blaNDM-1 and its potential to spread between members of the family Enterobacteriaceae and A. baumannii.
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Affiliation(s)
- Ying-Min Huang
- Department of Immunology, Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China Department of Laboratory, Central Hospital of Panyu District, Shiqiao, Guangzhou, Guangdong, China
| | - Lan-Lan Zhong
- Department of Immunology, Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Xue-Fei Zhang
- Department of Immunology, Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
| | - Hang-Tong Hu
- Department of Immunology, Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Yu-Qi Li
- Department of Immunology, Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xiao-Rong Yang
- Clinical Laboratory of the First Affiliated Hospital of Guangdong Pharmaceutical University, Guangzhou, China
| | - Lian-Qiang Feng
- Department of Immunology, Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Xi Huang
- Department of Immunology, Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou, China
| | - Guo-Bao Tian
- Department of Immunology, Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou, China
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Flórez AB, Mayo B. The Plasmid Complement of the Cheese Isolate Lactococcus garvieae IPLA 31405 Revealed Adaptation to the Dairy Environment. PLoS One 2015; 10:e0126101. [PMID: 25942497 PMCID: PMC4420470 DOI: 10.1371/journal.pone.0126101] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 03/29/2015] [Indexed: 01/21/2023] Open
Abstract
Lactococcus garvieae is a lactic acid bacterium found in raw-milk dairy products as well as a range of aquatic and terrestrial environments. The plasmids in L. garvieae have received little attention compared to those of dairy Lactococcus lactis, in which the genes carried by these extrachromosomal elements are considered of adaptive value. The present work reports the sequencing and analysis of the plasmid complement of L. garvieae IPLA 31405, a strain isolated from a traditional, Spanish, starter-free cheese made from raw-milk. It consists of pLG9 and pLG42, of 9,124 and 42,240 nucleotides, respectively. Based on sequence and structural homology in the putative origin of replication (ori) region, pLG9 and pLG42 are predicted to replicate via a theta mechanism. Real-time, quantitative PCR showed the number of copies per chromosome equivalent of pLG9 and pLG42 to be around two and five, respectively. Sequence analysis identified eight complete open reading frames (orfs) in pLG9 and 36 in pLG42; these were organized into functional modules or cassettes containing different numbers of genes. These modules were flanked by complete or interrupted insertion sequence (IS)-like elements. Among the modules of pLG42 was a gene cluster encoding specific components of a phosphoenolpyruvate-phosphotransferase (PEP-PTS) system, including a phospho-β-galacosidase. The cluster showed a complete nucleotide identity respect to that in plasmids of L. lactis. Loss of pLG42 showed this to be involved in lactose assimilation. In the same plasmid, an operon encoding a type I restriction/modification (R/M) system was also identified. The specificity of this R/M system might be broadened by different R/M specificity subunits detected in pLG9 and in the bacterial chromosome. However, challenges of L. garvieae IPLA 31405 against L. lactis phages proved that the R/M system was not involved in phage resistance. Together, these results support the hypothesis that, as in L. lactis, pLG42 contribute towards the adaptation of L. garvieae to the dairy environment.
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Affiliation(s)
- Ana Belén Flórez
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Carretera de Infiesto, s/n, 33300-Villaviciosa, Asturias, Spain
| | - Baltasar Mayo
- Departamento de Microbiología y Bioquímica, Instituto de Productos Lácteos de Asturias (IPLA-CSIC), Carretera de Infiesto, s/n, 33300-Villaviciosa, Asturias, Spain
- * E-mail:
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Moleres J, Santos-López A, Lázaro I, Labairu J, Prat C, Ardanuy C, González-Zorn B, Aragon V, Garmendia J. Novel blaROB-1-bearing plasmid conferring resistance to β-lactams in Haemophilus parasuis isolates from healthy weaning pigs. Appl Environ Microbiol 2015; 81:3255-67. [PMID: 25747001 PMCID: PMC4393459 DOI: 10.1128/aem.03865-14] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Accepted: 02/25/2015] [Indexed: 11/20/2022] Open
Abstract
Haemophilus parasuis, the causative agent of Glässer's disease, is one of the early colonizers of the nasal mucosa of piglets. It is prevalent in swine herds, and lesions associated with disease are fibrinous polyserositis and bronchopneumonia. Antibiotics are commonly used in disease control, and resistance to several antibiotics has been described in H. parasuis. Prediction of H. parasuis virulence is currently limited by our scarce understanding of its pathogenicity. Some genes have been associated with H. parasuis virulence, such as lsgB and group 1 vtaA, while biofilm growth has been associated with nonvirulent strains. In this study, 86 H. parasuis nasal isolates from farms that had not had a case of disease for more than 10 years were obtained by sampling piglets at weaning. Isolates were studied by enterobacterial repetitive intergenic consensus PCR and determination of the presence of lsgB and group 1 vtaA, biofilm formation, inflammatory cell response, and resistance to antibiotics. As part of the diversity encountered, a novel 2,661-bp plasmid, named pJMA-1, bearing the blaROB-1 β-lactamase was detected in eight colonizing strains. pJMA-1 was shown to share a backbone with other small plasmids described in the Pasteurellaceae, to be 100% stable, and to have a lower biological cost than the previously described plasmid pB1000. pJMA-1 was also found in nine H. parasuis nasal strains from a separate collection, but it was not detected in isolates from the lesions of animals with Glässer's disease or in nontypeable Haemophilus influenzae isolates. Altogether, we show that commensal H. parasuis isolates represent a reservoir of β-lactam resistance genes which can be transferred to pathogens or other bacteria.
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Affiliation(s)
- Javier Moleres
- Instituto de Agrobiotecnología, CSIC-Universidad Pública Navarra-Gobierno de Navarra, Mutilva, Spain
| | - Alfonso Santos-López
- Departamento de Sanidad Animal, Facultad de Veterinaria y VISAVET, Universidad Complutense, Madrid, Spain
| | - Isidro Lázaro
- Instituto Navarro de Tecnologías e Infraestructuras Agroalimentarias-INTIA, Navarra, Spain
| | - Javier Labairu
- Instituto Navarro de Tecnologías e Infraestructuras Agroalimentarias-INTIA, Navarra, Spain
| | - Cristina Prat
- Hospital Universitari Germans Trias i Pujol, Badalona, Spain Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Carmen Ardanuy
- Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain Hospital Universitari Bellvitge, Barcelona, Spain
| | - Bruno González-Zorn
- Departamento de Sanidad Animal, Facultad de Veterinaria y VISAVET, Universidad Complutense, Madrid, Spain
| | - Virginia Aragon
- Centre de Recerca en Sanitat Animal (CReSA), Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Campus de la Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Junkal Garmendia
- Instituto de Agrobiotecnología, CSIC-Universidad Pública Navarra-Gobierno de Navarra, Mutilva, Spain Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
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Riojas MA, Kiss K, McKee ML, Hazbón MH. Multiplex PCR for species-level identification of Bacillus anthracis and detection of pXO1, pXO2, and related plasmids. Health Secur 2015; 13:122-9. [PMID: 25813976 DOI: 10.1089/hs.2014.0056] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Bacillus anthracis virulence plasmids pXO1 and pXO2 have critical implications for biosafety and select agent status. The proper identification and characterization of B. anthracis and its plasmid profile is important to the biodefense research community. Multiplex PCR was used to simultaneously detect a B. anthracis-specific chromosomal mutation, 4 targets distributed across pXO1, 3 targets distributed across pXO2, and highly conserved regions of the 16S gene, allowing an internal positive control for each sample. The multiplex PCR can produce as many as 9 easily separable and distinguishable amplicons, ranging in size from 188 to 555 bp. The PCR results were used to characterize DNA samples extracted from B. anthracis, other Bacillus species, and other bacterial species from many different genera. With the exception of 2 novel putative plasmids discovered, testing against inclusion and extensive exclusion panels showed 100% correlation to previously published and expected results. Upon testing 29 previously unpublished B. anthracis strains, 10 (34.5%) were pXO1(+)/pXO2(+), 9 (31.0%) were pXO1(+)/pXO2(-), 7 (24.1%) were pXO1(-)/pXO2(+), and 3 (10.3%) were pXO1(-)/pXO2(-). The present work presents a novel 9-target multiplex PCR assay capable of species-level identification of B. anthracis via a unique chromosomal marker and the detection of pXO1 and pXO2 via multiply redundant targets on each.
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Korotaieva N V, Limanska N V. [Detection of pathogenic bacteria Rhizobium vitis in vineyards of the south of Ukraine]. Mikrobiol Z 2015; 77:28-32. [PMID: 26036030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The total number of microbiota from grape crown gall tissues ranged from (2,3 ± 0.8) x 10(3) to (7.3 ± 0.4) x 10(5) CFU/g. The amount of bacteria from Rhizobium genus reached from (1.2 ±0.2) x 10(2) to (2.1 ± 0.2) x 10(4) CFU/g depending on a tested plant. It was found out that only a small percentage of the strains (3.1 - 4.9%) were oncogenic. New pathogenic strains (R. vitis ONU388, R. vitis ONU389 and R. vitis ONU390) possessing plasmid genes of pathogenicity virC, ipt and virD2 were isolated.
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Barkova IA, Novozhenina AV, Barkov AM, Porokhnia SV, Tkachenko GA, Lipnitskiĭ AV. [Characteristics of isogenic variants of Bacillus anthracis with various content of virulence plasmids]. Zh Mikrobiol Epidemiol Immunobiol 2015:17-22. [PMID: 25842948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
AIM Production and characteristics by main cultural-morphologic and antigenic properties of isogenic variants Bacillus anthracis, that differ by the presence of virulence plasmids. MATERIALS AND METHODS B. anthracis 81/1, 575/122 virulent and B. anthracis STI, 55, Sterne vaccine strains were used in the study. Isogenic variants, that differ by the presence of virulence plasmids, were obtained by temperature elimination of plasmids, as well as during cultivation of anthrax strains in medium with kanamycin. The strains were characterized by cultural-morphologic, biochemical properties. The presence of virulence plasmids was determined by polymerase chain reaction method. Antigenic properties were studied in immune diffusion reaction with growing cultures with sera against protective antigen and S-layer proteins, electrophoresis, immune blotting. RESULTS Isogenic variants were produced from virulent strains B. anthracis 81/1, 575/122 and vaccine strains STI, 55, Sterne: mono-plasmid toxin-producing (81/1 R01, 575/122 R01) and capsule-containing (81/1 R02, 575/122 R02), and plasmid-less (81/1 R00, 575/122 R00, STI R00, 55 R00, Sterne R00), that differ by the presence of virulence plasmids. Strains had typical cultural-morphologic properties, differed by biochemical and antigenic properties. Cultural filtrates of toxin-producing strains had protein of anthrax toxin; plasmid-less strains--had proteins, that had molecular masses corresponding to molecular masses of S-layer EA1 and Sap proteins. CONCLUSION These strains may be used to study variability and proteomic analysis of anthrax causative agent, as well as for isolation of antigens with the aim of evaluating their immune diagnostic significance.
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Jang MS, Fujita A, Ikawa S, Hanawa K, Yamamura H, Tamura T, Hayakawa M, Tezuka T, Ohnishi Y. Isolation of a novel plasmid from Couchioplanes caeruleus and construction of two plasmid vectors for gene expression in Actinoplanes missouriensis. Plasmid 2014; 77:32-8. [PMID: 25500016 DOI: 10.1016/j.plasmid.2014.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 11/22/2014] [Accepted: 12/01/2014] [Indexed: 11/15/2022]
Abstract
To date, no plasmid vector has been developed for the rare actinomycete Actinoplanes missouriensis. Moreover, no small circular plasmid has been reported to exist in the genus Actinoplanes. Here, a novel plasmid, designated pCAZ1, was isolated from Couchioplanes caeruleus subsp. azureus via screening for small circular plasmids in Actinoplanes (57 strains) and Couchioplanes (2 strains). Nucleotide sequencing revealed that pCAZ1 is a 5845-bp circular molecule with a G + C content of 67.5%. The pCAZ1 copy number was estimated at 30 per chromosome. pCAZ1 contains seven putative open reading frames, one of which encodes a protein containing three motifs conserved among plasmid-encoded replication proteins that are involved in the rolling-circle mechanism of replication. Detection of single-stranded DNA intermediates in C. caeruleus confirmed that pCAZ1 replicates by this mechanism. The ColE1 origin from pBluescript SK(+) and the oriT sequence with the apramycin resistance gene aac(3)IV from pIJ773 were inserted together into pCAZ1, to construct the Escherichia coli-A. missouriensis shuttle vectors, pCAM1 and pCAM2, in which the foreign DNA fragment was inserted into pCAZ1 in opposite directions. pCAM1 and pCAM2 were successfully transferred to A. missouriensis through the E. coli-mediated conjugative transfer system. The copy numbers of pCAM1 and pCAM2 in A. missouriensis were estimated to be one and four per chromosome, respectively. Thus, these vectors can be used as effective genetic tools for homologous and heterologous gene expression studies in A. missouriensis.
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Affiliation(s)
- Moon-Sun Jang
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Azusa Fujita
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Satomi Ikawa
- Division of Applied Biological Sciences, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Keitaro Hanawa
- Division of Applied Biological Sciences, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Hideki Yamamura
- Division of Applied Biological Sciences, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Tomohiko Tamura
- Biological Resource Center, National Institute of Technology and Evaluation (NBRC), 2-5-8 Kazusakamatari, Kisarazu, Chiba 292-0818, Japan
| | - Masayuki Hayakawa
- Division of Applied Biological Sciences, University of Yamanashi, 4-3-11 Takeda, Kofu, Yamanashi 400-8511, Japan
| | - Takeaki Tezuka
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Yasuo Ohnishi
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.
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Falgenhauer L, Schmiedel J, Ghosh H, Fritzenwanker M, Yao Y, Bauerfeind R, Imirzalioglu C, Chakraborty T. Resistance plasmids in ESBL-encoding Escherichia coli isolates from humans, dogs and cats. Berl Munch Tierarztl Wochenschr 2014; 127:458-463. [PMID: 25872255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We characterized ESBL-producing Escherichia coli isolates from diseased dog, cat and human sources for their plasmid content. Plasmids with different Inc groups and combinations of resistance genes were detected in these isolates. The pan-genome of the plasmid-associated genes was found to be large, indicating diversity of the gene pool among the plasmids. No commonly occurring plasmids with similar gene content in isolates from dog, cats and humans were detected.
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Grandhi TSP, Mallik A, Lin KN, Miryala B, Potta T, Tian Y, Rege K. Aminoglycoside antibiotic-derived anion-exchange microbeads for plasmid DNA binding and in situ DNA capture. ACS Appl Mater Interfaces 2014; 6:18577-89. [PMID: 25314226 DOI: 10.1021/am503240q] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Plasmid DNA (pDNA) therapeutics are being investigated for gene therapy and DNA vaccines against diseases including cancer, cystic fibrosis and AIDS. In addition, several applications in modern biotechnology require pDNA for transient protein production. Here, we describe the synthesis, characterization, and evaluation of microbeads ("Amikabeads") derived from the aminoglycoside antibiotic amikacin for pDNA binding and in situ DNA capture from mammalian cells. The parental aminoglycoside-derived microbeads (Amikabeads-P) acted as anion-exchange materials, and demonstrated high capacities for binding pDNA. Binding of pDNA was significantly enhanced following quaternization of the amines on the microbeads (Amikabeads-Q). Amikabeads were further employed for the disruption and extraction of DNA from mammalian cells, indicating their utility for in situ DNA capture. Our results indicate that Amikabeads are a novel material, with multiple reactive groups for further conjugation, and can have several applications in plasmid DNA biotechnology.
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Affiliation(s)
- Taraka Sai Pavan Grandhi
- Harrington Biomedical Engineering, School of Biological and Health Systems Engineering ‡Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University , Tempe, Arizona 85287, United States
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Norman A, Riber L, Luo W, Li LL, Hansen LH, Sørensen SJ. An improved method for including upper size range plasmids in metamobilomes. PLoS One 2014; 9:e104405. [PMID: 25116381 PMCID: PMC4130580 DOI: 10.1371/journal.pone.0104405] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Accepted: 07/14/2014] [Indexed: 12/24/2022] Open
Abstract
Two recently developed isolation methods have shown promise when recovering pure community plasmid DNA (metamobilomes/plasmidomes), which is useful in conducting culture-independent investigations into plasmid ecology. However, both methods employ multiple displacement amplification (MDA) to ensure suitable quantities of plasmid DNA for high-throughput sequencing. This study demonstrates that MDA greatly favors smaller circular DNA elements (<10 Kbp), which, in turn, leads to stark underrepresentation of upper size range plasmids (>10 Kbp). Throughout the study, we used two model plasmids, a 4.4 Kbp cloning vector (pBR322), and a 56 Kbp conjugative plasmid (pKJK10), to represent lower- and upper plasmid size ranges, respectively. Subjecting a mixture of these plasmids to the overall isolation protocol revealed a 34-fold over-amplification of pBR322 after MDA. To address this bias, we propose the addition of an electroelution step that separates different plasmid size ranges prior to MDA in order to reduce size-dependent competition during incubation. Subsequent analyses of metamobilome data from wastewater spiked with the model plasmids showed in silica recovery of pKJK10 to be very poor with the established method and a 1,300-fold overrepresentation of pBR322. Conversely, complete recovery of pKJK10 was enabled with the new modified protocol although considerable care must be taken during electroelution to minimize cross-contamination between samples. For further validation, non-spiked wastewater metamobilomes were mapped to more than 2,500 known plasmid genomes. This displayed an overall recovery of plasmids well into the upper size range (median size: 30 kilobases) with the modified protocol. Analysis of de novo assembled metamobilome data also suggested distinctly better recovery of larger plasmids, as gene functions associated with these plasmids, such as conjugation, was exclusively encoded in the data output generated through the modified protocol. Thus, with the suggested modification, access to a large uncharacterized pool of accessory elements that reside on medium-to-large plasmids has been improved.
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Affiliation(s)
- Anders Norman
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Department of Earth and Planetary Science, University of California, Berkeley, California, United States of America
| | - Leise Riber
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Wenting Luo
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Li Li Li
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lars Hestbjerg Hansen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
- Department of Environmental Science, Aarhus University, Roskilde, Denmark
- * E-mail:
| | - Søren Johannes Sørensen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
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Kadnikov VV, Mardanov AV, Beleckiĭ AV, Karnachuk OV, Ravin NV. [Characteristics of the new plasmid, pMTB1, from the metagenome of the microbial community of underground thermal waters of Western Siberia]. Izv Akad Nauk Ser Biol 2014:236-240. [PMID: 25731033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A new circular 4935-bp long plasmid pMTB1 has been identified in sequences of the metagenome. The nucleotide sequence of pMTB1 is highly similar to that of plasmids, pME2001 and pME2200, from the methanogenic archaeon Methanothermobacter marburgensis. One of six putative protein-coding genes encodes a protein containing helix-turn-helix and ATP/GTP-binding motifs and, probably, functioning as a replication initiator protein. Homologs of other genes have been found only in the plasmids of M. marburgensis, but their functions are unknown. Comparison of the complete nucleotide sequences of the plasmids pMTB1, pME2001, and pME2200 has revealed that they have a common origin but differ from each other by the presence of several inserts flanked by nearly perfect direct repeats within regions not essential for replication.
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Abstract
Many techniques that are used to characterize individual RNA molecules can potentially alter the original transcript sequence or its posttranscriptional modifications, such as polyadenylation. Methods that are designed to define the ends of an RNA molecule, for example, oligonucleotide ligation, avoid altering the transcript sequence but can usually fulfill only one objective per experiment (e.g., define the 5' or the 3' end). In contrast, not only does circularized reverse transcription coupled with PCR (cRT-PCR) preserve the original 5' and 3' ends of the transcript and posttranscriptionally added extensions, but also the material from one experimental procedure can be utilized in order to characterize both the 5' and 3' ends. Furthermore, if suitable oligonucleotide primers are designed, cRT-PCR can be used to isolate truncated, adenylated (and nonadenylated) molecules that are intermediates in RNA decay (Slomovic and Schuster, 2008).
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Affiliation(s)
- Shimyn Slomovic
- Biology Faculty, Technion Institute of Technology, Haifa, Israel
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Hong H, Ko HJ, Choi IG, Park W. Previously undescribed plasmids recovered from activated sludge confer tetracycline resistance and phenotypic changes to Acinetobacter oleivorans DR1. Microb Ecol 2014; 67:369-379. [PMID: 24337108 DOI: 10.1007/s00248-013-0343-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 12/02/2013] [Indexed: 06/03/2023]
Abstract
We used culture-dependent and culture-independent methods to extract previously undescribed plasmids harboring tetracycline (TC) resistance genes from activated sludge. The extracted plasmids were transformed into naturally competent Acinetobacter oleivorans DR1 to recover a non-Escherichia coli-based plasmid. The transformed cells showed 80-100-fold higher TC resistance than the wild-type strain. Restriction length polymorphism performed using 30 transformed cells showed four different types of plasmids. Illumina-based whole sequencing of the four plasmids identified three previously unreported plasmids and one previously reported plasmid. All plasmids carried TC resistance-related genes (tetL, tetH), tetracycline transcriptional regulators (tetR), and mobilization-related genes. As per expression analysis, TC resistance genes were functional in the presence of TC. The recovered plasmids showed mosaic gene acquisition through horizontal gene transfer. Membrane fluidity, hydrophobicity, biofilm formation, motility, growth rate, sensitivity to stresses, and quorum sensing signals of the transformed cells were different from those of the wild-type cells. Plasmid-bearing cells seemed to have an energy burden for maintaining and expressing plasmid genes. Our data showed that acquisition of TC resistance through plasmid uptake is related to loss of biological fitness. Thus, cells acquiring antibiotic resistance plasmids can survive in the presence of antibiotics, but must pay ecological costs.
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Affiliation(s)
- Hyerim Hong
- Department of Environmental Science and Ecological Engineering, Korea University, Anam-Dong 5Ga, Seungbuk-Ku, Seoul, 136-713, Republic of Korea
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Abstract
The following describes noncommercial methods for the purification of genomic and plasmid DNA from S. epidermidis. These include both large-scale, high molecular weight and quick, small-scale chromosomal DNA extractions, and also a standard alkaline lysis method of plasmid preparation.
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Affiliation(s)
- Jill K Lindgren
- Department of Pathology and Microbiology, Center for Staphylococcal Research, University of Nebraska Medical Center, Omaha, NE, USA
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Abstract
The BioBrick idea was developed to introduce the engineering principles of abstraction and standardization into synthetic biology. BioBricks are DNA sequences that serve a defined biological function and can be readily assembled with any other BioBrick parts to create new BioBricks with novel properties. In order to achieve this, several assembly standards can be used. Which assembly standards a BioBrick is compatible with, depends on the prefix and suffix sequences surrounding the part. In this chapter, five of the most common assembly standards will be described, as well as some of the most used assembly techniques, cloning procedures, and a presentation of the available software tools that can be used for deciding on the best method for assembling of different BioBricks, and searching for BioBrick parts in the Registry of Standard Biological Parts database.
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Affiliation(s)
- Gunvor Røkke
- Department of Biotechnology, Norwegian University of Science and Technology (NTU), Trondheim, Norway
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47
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Abstract
For pharmaceutical applications of plasmid DNA, either direct or indirect, certain quality standards are required. Whereas for direct gene transfer into human "Good Manufacturing Practice" (GMP) grade is mandatory, for GMP production of, e.g., viral vectors (AAV, etc.) the plasmid DNA used needs not necessarily be produced under GMP. Besides such regulatory aspects up-scaling of the plasmid DNA production process from research laboratory scale (up to a few milligrams) to industrial scales (milligram to gram scales) is an issue that is addressed here.
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Affiliation(s)
- Marco Schmeer
- PlasmidFactory GmbH & Co. KG, Meisenstr. 96, D-33607, Bielefeld, Germany
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Abstract
Plasmid DNA for immunization applications must be of the highest purity and quality. The ability of downstream purification to efficiently produce a pure final product is directly influenced by the performance of the upstream fermentation process. While several clinical manufacturing facilities already have validated fermentation processes in place to manufacture plasmid DNA for use in humans, a simple and inexpensive laboratory-scale fermentation process can be valuable for in-house production of plasmid DNA for use in animal efficacy studies. This chapter describes a simple fed-batch fermentation process for producing bacterial cell paste enriched with high-quality plasmid DNA. A constant feeding strategy results in a medium cell density culture with continuously increasing plasmid amplification towards the end of the process. Cell banking and seed culture preparation protocols, which can dramatically influence final product yield and quality, are also described. These protocols are suitable for production of research-grade plasmid DNA at the 100 mg-to-1.5 g scale from a typical 10 L laboratory benchtop fermentor.
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Affiliation(s)
- Aaron E Carnes
- Nature Technology Corporation, 4701 Innovation Drive, Lincoln, NE, 68521, USA,
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Abstract
Reverse transcription combined with the polymerase chain reaction (RT-PCR) is a viable method widely used to quantify gene expression. There are two ways to quantify gene expression by real-time PCR: relative quantification and absolute quantification. Relative quantification relates the PCR signal of the target gene to a control gene, normally a housekeeping gene. Absolute quantification determines the input copy number, usually by relating the PCR signal to a standard curve. Here we describe both methods from RNA extraction to its quantification by real-time PCR.
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Affiliation(s)
- Roberta Mazza
- Department of Veterinary Medicine, University of Sassari, Via Vienna 2, 07100, Sassari, Italy,
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Bilchenko AV, Chub OI. [Prevalence of Types TEM, SHV and CTX-M βLES Among Pathogens of Chronic Pyelonephritis]. Antibiot Khimioter 2014; 59:24-26. [PMID: 26448990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
There is lately observed an increase in the resistance of the main pathogens of urologic infection to β-lactam antibiotics due to production of plasmid-induced β-lactamases. The aim of the study was to reveal types TEM, SHV and CTX-M plasmid β-lactamases among uropathogens. Out of 115 isolates, 30 (26.1%) strains produced β-lactamases. Genes blaTEM and bla CTX-Mwere the most frequent. Most of the isolates were resistant to ampicillin (73.3%), ciprofloxacin (46.7%), levofloxacin (43.3%), gentamicin (40%). The βLES-producing strains were susceptible to meropenem (96.7%), nitroxolin (83.3%), phosphomycin (70%), amikacin (70%). The presence of the resistance genes in the uropathogens was evident of a high rate of their distribution among them by the plasmids. Detection of the plasmid-induced β-lactamases is important for the optimal choice of the antibiotic for empirical therapy.
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