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Kodackattumannil P, Sasi S, Krishnan S, Lekshmi G, Kottackal M, Amiri KMA. Protocol for the High-quality Plasmid Isolation from Different Recalcitrant Bacterial Species: Agrobacterium spp. , Rhizobium sp., and Bacillus thuringiensis. Bio Protoc 2023; 13:e4788. [PMID: 37575390 PMCID: PMC10415192 DOI: 10.21769/bioprotoc.4788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/10/2023] [Accepted: 06/18/2023] [Indexed: 08/15/2023] Open
Abstract
High yield of good quality plasmid DNA from gram -ve bacteria (Agrobacterium tumefaciens, A. rhizogenes, and Rhizobium sp.) and gram +ve bacterium (Bacillus thuringiensis) is difficult. The widely used plasmid extraction kits for Escherichia coli yield a low quantity of poor-quality plasmid DNA from these species. We have optimized an in-house modification of the QIAprep Spin Miniprep kit protocol of Qiagen, consisting of two extraction steps. In the first, the centrifugation after adding neutralization buffer is followed by ethanol (absolute) precipitation of plasmid DNA. In the second extraction step, the precipitated DNA is dissolved in Tris-EDTA (TE) buffer, followed by an addition of 0.5 volumes of 5 M sodium chloride and 0.1 volumes of 20% (w/v) sodium dodecyl sulfate. After incubation at 65 °C for 15 min, the plasmid DNA is extracted with an equal volume of chloroform:isoamyl alcohol (CIA). RNase (20 mg/mL) is added to the upper phase retrieved after centrifugation and is incubated at 37 °C for 15 min. The extraction of the plasmid DNA with an equal volume of CIA is followed by centrifugation and is precipitated from the retrieved upper phase by adding an equal volume of absolute ethanol. The pellet obtained after centrifugation is washed twice with 70% (v/v) ethanol, air dried, dissolved in TE buffer, and quantified. This easy-to-perform protocol is free from phenol extraction, density gradient steps, and DNA binding columns, and yields high-quality plasmid DNA. The protocol opens an easy scale up to yield a large amount of high-quality plasmid DNA, useful for high-throughput downstream applications. Key features The protocol is free from density gradient steps and use of phenol. The protocol is an extension of the QIAprep Spin Miniprep kit (Qiagen) and is applicable for plasmid DNA isolation from difficult-to-extract bacterial species. The protocol facilitates the direct transformation of the ligation product into Agrobacterium by skipping the step of E. coli transformation. The plasmids isolated are of sequencing grade and the method is useful for extracting plasmids for metagenomic studies. Graphical overview Overview of the plasmid isolation protocol (modified QIAprep Spin Miniprep kit) of the present study.
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Affiliation(s)
- Preshobha Kodackattumannil
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Shina Sasi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Saranya Krishnan
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Geetha Lekshmi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Martin Kottackal
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Khaled M. A. Amiri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
- Department of Biology, College of Science, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
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Alabed D, Huo N, Gu Y, Thomson JG. Complete Genome of Agrobacterium fabrum Strain 1D1416. Microbiol Resour Announc 2023:e0026423. [PMID: 37338417 DOI: 10.1128/mra.00264-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/01/2023] [Indexed: 06/21/2023] Open
Abstract
This work reports the draft genome of Agrobacterium fabrum strain 1D1416. The assembled genome is composed of a 2,837,379-bp circular chromosome, a 2,043,296-bp linear chromosome, a 519,735-bp AT1 plasmid, a 188,396-bp AT2 plasmid, and a 196,706-bp Ti virulence plasmid. The nondisarmed strain produces gall-like structures in citrus tissue.
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Affiliation(s)
- Diaa Alabed
- USDA-ARS Crop Improvement and Genetics, Western Regional Research Center, Albany, California, USA
| | - Naxin Huo
- USDA-ARS Crop Improvement and Genetics, Western Regional Research Center, Albany, California, USA
- Department of Plant Sciences, University of California, Davis, California, USA
| | - Yong Gu
- USDA-ARS Crop Improvement and Genetics, Western Regional Research Center, Albany, California, USA
| | - James G Thomson
- USDA-ARS Crop Improvement and Genetics, Western Regional Research Center, Albany, California, USA
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Rajendran K, Kumar V, Raja I, Kumariah M, Tennyson J. Identification of sigma factor 54-regulated small non-coding RNAs by employing genome-wide and transcriptome-based methods in rhizobium strains. 3 Biotech 2022; 12:328. [PMID: 36276463 PMCID: PMC9584007 DOI: 10.1007/s13205-022-03394-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 10/12/2022] [Indexed: 11/01/2022] Open
Abstract
Rhizobium-legume symbiosis is considered as the major contributor of biological nitrogen fixation. Bacterial small non-coding RNAs are crucial regulators in several cellular adaptation processes that occur due to the changes in metabolism, physiology, or the external environment. Identifying and analysing the conditional specific/sigma factor-54 regulated sRNAs provides a better understanding of sRNA regulation/mechanism in symbiotic association. In the present study, we have identified sigma factor 54-regulated sRNAs from the genome of six rhizobium strains and from the RNA-seq data of free-living and symbiotic conditions of Bradyrhizobium diazoefficiens USDA 110 to identify the novel putative sRNAs that are over expressed during the regulation of nitrogen fixation. A total of 1351 sRNAs were predicted from the genome of six rhizobium strains and 1375 sRNAs were predicted from the transcriptome data of B. diazoefficiens USDA 110. Analysis of target mRNA for these novel sRNAs was inferred to target several nodulation and nitrogen fixation genes including nodC, nodJ, nodY, nodJ, nodM, nodW, nodZ, nifD, nifN, nifQ, fixK, fixL, fdx, nolB, and several cytochrome proteins. In addition, sRNAs of B. diazoefficiens USDA 110 which targeted the regulatory genes of nitrogen fixation were confirmed by wet-lab experiments with semi-quantitative reverse transcription polymerase chain reaction. Predicted target mRNAs were functionally classified based on the COG analysis and GO annotations. The genome-wide and transcriptome-based integrated methods have led to the identification of several sRNAs involved in the nodulation and symbiosis. Further validation of the functional role of these sRNAs can help in exploring the role of sRNAs in nitrogen metabolism during free-living and symbiotic association with legumes. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03394-x.
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Affiliation(s)
- Kasthuri Rajendran
- Department of Plant Morphology and Algology, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu 625 021 India
| | - Vikram Kumar
- Department of Plant Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu 625 021 India
| | - Ilamathi Raja
- Department of Plant Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu 625 021 India
| | - Manoharan Kumariah
- Department of Plant Morphology and Algology, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu 625 021 India
| | - Jebasingh Tennyson
- Department of Plant Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, Tamil Nadu 625 021 India
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Draft Genome Sequence of Agrobacterium fabrum Strain 1D1104. Microbiol Resour Announc 2021; 10:e0099621. [PMID: 34854699 PMCID: PMC8638575 DOI: 10.1128/mra.00996-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This work reports the draft genome sequence of Agrobacterium fabrum strain 1D1104. The assembled genome is composed of a 2,774,783-bp circular chromosome, a 2,110,112-bp linear chromosome, an AT plasmid of 133,577 bp, and four unassembled contigs of 5,389,544 bp, 42,391 bp, 41,768 bp, and 35,476 bp.
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Draft Genome Sequence of Agrobacterium tumefaciens Strain 1D1526. Microbiol Resour Announc 2019; 8:8/45/e01084-19. [PMID: 31699763 PMCID: PMC6838621 DOI: 10.1128/mra.01084-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This work reports the draft genome sequence of Agrobacterium tumefaciens strain 1D1526. The assembled genome is composed of a 2,881,823-bp circular chromosome, a 2,235,711-bp linear chromosome, and a 44,582-bp unassembled contig. This work reports the draft genome sequence of Agrobacterium tumefaciens strain 1D1526. The assembled genome is composed of a 2,881,823-bp circular chromosome, a 2,235,711-bp linear chromosome, and a 44,582-bp unassembled contig.
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Abstract
This work reports the draft genome sequence of Agrobacterium fabrum strain 1D159 (also known as ATCC strain 27912). The assembled genome is composed of a 2,861,352-bp circular chromosome, a 2,058,040-bp linear chromosome, a 519,735-bp AT plasmid, and the 223,394-bp Ti virulence plasmid. This work reports the draft genome sequence of Agrobacterium fabrum strain 1D159 (also known as ATCC strain 27912). The assembled genome is composed of a 2,861,352-bp circular chromosome, a 2,058,040-bp linear chromosome, a 519,735-bp AT plasmid, and the 223,394-bp Ti virulence plasmid. The wild nondisarmed strain produces small gall-like structures in citrus.
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Draft Genome Sequence of Serratia sp. 1D1416. Microbiol Resour Announc 2019; 8:MRA01354-18. [PMID: 30687823 PMCID: PMC6346155 DOI: 10.1128/mra.01354-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 12/14/2018] [Indexed: 11/23/2022] Open
Abstract
This work reports the draft genome of Serratia sp. 1D1416. The assembled genome contains a 5,552,016-bp circular chromosome. This work reports the draft genome of Serratia sp. 1D1416. The assembled genome contains a 5,552,016-bp circular chromosome. The strain was discovered in a mixed culture from a gall isolated from Euonymus japonicas.
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Nathoo N, Bernards MA, MacDonald J, Yuan ZC. A Hydroponic Co-cultivation System for Simultaneous and Systematic Analysis of Plant/Microbe Molecular Interactions and Signaling. J Vis Exp 2017. [PMID: 28784965 DOI: 10.3791/55955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
An experimental design mimicking natural plant-microbe interactions is very important to delineate the complex plant-microbe signaling processes. Arabidopsis thaliana-Agrobacterium tumefaciens provides an excellent model system to study bacterial pathogenesis and plant interactions. Previous studies of plant-Agrobacterium interactions have largely relied on plant cell suspension cultures, the artificial wounding of plants, or the artificial induction of microbial virulence factors or plant defenses by synthetic chemicals. However, these methods are distinct from the natural signaling in planta, where plants and microbes recognize and respond in spatial and temporal manners. This work presents a hydroponic cocultivation system where intact plants are supported by metal mesh screens and cocultivated with Agrobacterium. In this cocultivation system, no synthetic phytohormone or chemical that induces microbial virulence or plant defense is supplemented. The hydroponic cocultivation system closely resembles natural plant-microbe interactions and signaling homeostasis in planta. Plant roots can be separated from the medium containing Agrobacterium, and the signaling and responses of both the plant hosts and the interacting microbes can be investigated simultaneously and systematically. At any given timepoint/interval, plant tissues or bacteria can be harvested separately for various "omics" analyses, demonstrating the power and efficacy of this system. The hydroponic cocultivation system can be easily adapted to study: 1) the reciprocal signaling of diverse plant-microbe systems, 2) signaling between a plant host and multiple microbial species (i.e. microbial consortia or microbiomes), 3) how nutrients and chemicals are implicated in plant-microbe signaling, and 4) how microbes interact with plant hosts and contribute to plant tolerance to biotic or abiotic stresses.
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Affiliation(s)
- Naeem Nathoo
- London Research and Development Centre, Agriculture & Agri-Food Canada; Department of Biology, University of Western Ontario
| | | | | | - Ze-Chun Yuan
- London Research and Development Centre, Agriculture & Agri-Food Canada; Department of Microbiology and Immunology, University of Western Ontario;
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Draft Genome Sequence of Agrobacterium rhizogenes Strain NCPPB2659. GENOME ANNOUNCEMENTS 2016; 4:4/4/e00746-16. [PMID: 27469966 PMCID: PMC4966470 DOI: 10.1128/genomea.00746-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
This work reports the draft genome sequence of Agrobacterium rhizogenes strain NCPPB2659 (also known as strain K599). The assembled genome contains 5,277,347 bp, composed of one circular chromosome, the pRi2659 virulence plasmid, and 17 scaffolds pertaining to the linear chromosome. The wild-type strain causes hairy root disease in dicots and has been used to make transgenic hairy root cultures and composite plants (nontransgenic shoots with transgenic roots). Disarmed variants of the strain have been used to produce stable transgenic monocot and dicot plants.
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Abstract
Genetic modification of plants by the insertion of transgenes can be a powerful experimental approach to answer basic questions about gene product function. This technology can also be used to make improved crop varieties for use in the field. To apply this powerful tool to red clover, an important forage legume, a population of red clover with high potential for regeneration in tissue culture has been developed. Here we provide a detailed procedure for Agrobacterium-mediated transformation of genotypes derived from this regenerable population. We have successfully used this methodology to express β-glucuronidase (GUS) reporter genes as well as for hairpin RNA-mediated silencing of endogenous genes for polyphenol oxidase and a transferase crucial in phaselic acid accumulation.
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Affiliation(s)
- Michael L Sullivan
- Agricultural Research Service, U.S. Department of Agriculture, U.S. Dairy Forage Research Center, 1925 Linden Drive West, Madison, WI, 53706, USA,
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