1
|
Improved live-cell PCR method for detection of organophosphates degrading opd genes and applications. Appl Microbiol Biotechnol 2022; 106:1705-1714. [PMID: 35141867 DOI: 10.1007/s00253-022-11816-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 01/27/2022] [Accepted: 01/29/2022] [Indexed: 11/02/2022]
Abstract
Organophosphates are becoming an emerging pollutant due to their various applications, particularly as pesticides. In this study, an improved Colony (Live-cell) PCR method was developed for the detection of opd genes from bacteria encoding the organophosphate hydrolase enzymes capable of degrading various organophosphates. The improved method does not require pre-heating or pre-lysis of bacterial cells as essential in the conventional colony PCR. The reaction volume was scaled down to 10 µl by optimizing the PCR buffer and amplification conditions. The improved method was used for Gram positive and negative bacteria, glycerol stocks, liquid cultures, recombinant and mutant strains. Also, 16S rRNA gene was amplified from unknown environmental isolates and known E. coli strains. The amplified opd and 16S rRNA genes from the improved colony PCR method and by conventional PCR were sequenced, and similar results were obtained from both techniques. Thus, the improved method can be further explored in molecular biology or during biomarker studies. KEY POINTS: • Improved colony PCR method was developed for screening of opd genes from bacteria. • Method was validated for Gram positive/negative bacteria from solid as well as liquid media. • The improved method was rapid, efficient, and can be applied under various conditions.
Collapse
|
2
|
Rondelet A, Pozniakovsky A, Namboodiri D, Cardoso da Silva R, Singh D, Leuschner M, Poser I, Ssykor A, Berlitz J, Schmidt N, Röhder L, Vader G, Hyman AA, Bird AW. ESI mutagenesis: a one-step method for introducing mutations into bacterial artificial chromosomes. Life Sci Alliance 2020; 4:4/2/e202000836. [PMID: 33293335 PMCID: PMC7756954 DOI: 10.26508/lsa.202000836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/23/2020] [Accepted: 11/23/2020] [Indexed: 01/23/2023] Open
Abstract
A simple and efficient recombineering-based method for introducing point mutations into bacterial artificial chromosomes using an artificial intron cassette. Bacterial artificial chromosome (BAC)–based transgenes have emerged as a powerful tool for controlled and conditional interrogation of protein function in higher eukaryotes. Although homologous recombination-based recombineering methods have streamlined the efficient integration of protein tags onto BAC transgenes, generating precise point mutations has remained less efficient and time-consuming. Here, we present a simplified method for inserting point mutations into BAC transgenes requiring a single recombineering step followed by antibiotic selection. This technique, which we call exogenous/synthetic intronization (ESI) mutagenesis, relies on co-integration of a mutation of interest along with a selectable marker gene, the latter of which is harboured in an artificial intron adjacent to the mutation site. Cell lines generated from ESI-mutated BACs express the transgenes equivalently to the endogenous gene, and all cells efficiently splice out the synthetic intron. Thus, ESI mutagenesis provides a robust and effective single-step method with high precision and high efficiency for mutating BAC transgenes.
Collapse
Affiliation(s)
- Arnaud Rondelet
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Andrei Pozniakovsky
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | | | | - Divya Singh
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Marit Leuschner
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Ina Poser
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Andrea Ssykor
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Julian Berlitz
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Nadine Schmidt
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Lea Röhder
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Gerben Vader
- Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | | |
Collapse
|
3
|
Lyozin GT, Brunelli L. DNA gap repair in Escherichia coli for multiplex site-directed mutagenesis. FASEB J 2020; 34:6351-6368. [PMID: 32167210 DOI: 10.1096/fj.201902260r] [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: 09/03/2019] [Revised: 01/22/2020] [Accepted: 03/01/2020] [Indexed: 11/11/2022]
Abstract
Site-directed mutagenesis allows the generation of novel DNA sequences that can be used for a variety of important applications such as the functional analysis of genetic variants. To overcome the limitations of existing site-directed mutagenesis approaches, we explored in vivo DNA gap repair. We found that site-specific mutations in plasmid DNA can be generated in Escherichia coli using mutant single-stranded oligonucleotides to target PCR-derived linear double-stranded plasmid DNA. We called this method DeGeRing, and we characterized its advantages, including non-biased multiplex mutagenesis, over existing site-directed mutagenesis methods such as recombineering (recombination-mediated genetic engineering), single DNA break repair (SDBR, introduced by W. Mandecki), and QuikChange (Agilent Technologies, La Jolla, CA). We determined the efficiency of DeGeRing to induce site-directed mutations with and without a phenotype in three K-12 E coli strains using multiple single-stranded oligonucleotides containing homological and heterological parts of various sizes. Virtual lack of background made the isolation of mutants with frequencies up to 10-6 unnecessary. Our data show that endogenous DNA gap repair in E coli supports efficient multiplex site-directed mutagenesis. DeGeRing might facilitate the generation of mutant DNA sequences for protein engineering and the functional analysis of genetic variants in reverse genetics.
Collapse
Affiliation(s)
- George T Lyozin
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE, USA.,Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Luca Brunelli
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE, USA.,Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| |
Collapse
|
4
|
Lyozin GT, Brunelli L. Live-cell PCR and one-step purification streamline DNA engineering. FASEB J 2020; 34:3448-3460. [PMID: 31944382 DOI: 10.1096/fj.201902261r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/21/2019] [Accepted: 12/16/2019] [Indexed: 01/12/2023]
Abstract
In vivo DNA engineering such as recombineering (recombination-mediated genetic engineering) and DNA gap repair typically involve growing Escherichia coli (E coli) containing plasmids, followed by plasmid DNA extraction and purification prior to downstream PCR-mediated DNA modifications and DNA sequencing. We previously demonstrated that crude cell lysates could be used for some limited downstream DNA applications. Here, we show how live E coli cell PCR and one-step LiCl-isopropanol purification can streamline DNA engineering. In DNA gap repair, live-cell PCR allowed the convenient elimination of clones containing background plasmids prior to DNA sequencing. Live-cell PCR also enabled the generation of specific DNA sequences for DNA engineering up to 11 kilo base pairs in length and with up to 80 base pair terminal non-homology. Using gel electrophoresis and DNA melting curve analysis, we showed that LiCl-isopropanol DNA precipitation removed primers and small, nonspecific PCR products from live-cell PCR products in only ~10-minutes. DNA sequencing of purified products yielded Phred quality scores values of ~55%. These data indicate that live-cell PCR and LiCl-isopropanol DNA precipitation are ideal to prepare DNA for sequencing and other downstream DNA applications, and might therefore accelerate high-throughput DNA engineering pipelines.
Collapse
Affiliation(s)
- George T Lyozin
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE, USA.,Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Luca Brunelli
- Department of Pediatrics, University of Nebraska Medical Center, Omaha, NE, USA.,Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| |
Collapse
|
5
|
Jothiramshekar S, Benjamin JJ, Krishnasamy R, George S, Swaminathan R, Parida A. Identification of salt-responsive genes from C4 halophyte Suaeda nudiflora through suppression subtractive hybridization and expression analysis under individual and combined treatment of salt and elevated carbon dioxide conditions. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:163-172. [PMID: 32158127 PMCID: PMC7036381 DOI: 10.1007/s12298-019-00722-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/10/2019] [Accepted: 10/14/2019] [Indexed: 06/10/2023]
Abstract
Salinization of soil is a prime abiotic stress that limits agriculture productivity worldwide. To Study the mechanisms that halophytes take up to survive under high salt condition is important in engineering salinity stress tolerance in sensitive species. Suaeda nudiflora is a halophyte plant that grows in the saline environment and extreme high tidal belt. The species have high capability to produce high protein biomass in salty soils due to C4 photosynthesis. The physiological and biochemical changes in S. nudiflora under salinity stress were studied by measuring chlorophyll content, electrolytic leakage, level of lipid peroxidation and total soluble sugars. Increased lipid peroxidation and electrolytic leakage was observed in salt stressed S. nudiflora compared to control plants. A suppression subtractive hybridization strategy was employed to identify differentially expressed genes under salt treatment in S. nudiflora. A total of 333 positive clones were identified and screened. Of these, 250 expressed sequence tags were identified. cDNA subtraction library resulted in 33 contigs and 138 singletons. The functional annotation and metabolic pathways identification were performed using the Blast2GO program. In addition, we analyzed the expression patterns of 18 genes associated with salt stress-responsive pathways by semi-quantitative PCR under salt and elevated carbon dioxide (CO2) conditions. Several of the analyzed genes showed an increase in expression levels under different time points of salt treatment and at different concentrations of salt. When the same genes were studied for its expression under elevated CO2 concentrations, most of the known salt responsive genes showed higher expression under the combined treatment of elevated CO2 concentrations (500 ppm) and NaCl treatment (200 mM) compare to ambient condition. This implies that salt responsive genes are enhanced at elevated CO2 concentrations.
Collapse
Affiliation(s)
| | | | - Rani Krishnasamy
- M. S. Swaminathan Research Foundation, Chennai, Tamil Nadu India
| | - Suja George
- M. S. Swaminathan Research Foundation, Chennai, Tamil Nadu India
| | | | - Ajay Parida
- Institute of Life Sciences, Bhubaneswar, India
| |
Collapse
|
6
|
Lyozin GT, Kosaka Y, Bhattacharje G, Yost HJ, Brunelli L. Direct Isolation of Seamless Mutant Bacterial Artificial Chromosomes. ACTA ACUST UNITED AC 2017; 118:8.6.1-8.6.29. [PMID: 28369677 DOI: 10.1002/cpmb.34] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Seamless (i.e., without unwanted DNA sequences) mutant bacterial artificial chromosomes (BACs) generated via recombination-mediated genetic engineering (recombineering) are better suited to study gene function compared to complementary DNA (cDNA) because they contain only the specific mutation and provide all the regulatory sequences required for in vivo gene expression. However, precisely mutated BACs are typically rare (∼1:1,000 to 1:100,000), making their isolation quite challenging. Although these BACs have been classically isolated by linking the mutation to additional genes, i.e., selectable markers, this approach is prone to false positives and is labor-intensive because it requires the subsequent removal of the selectable marker. We created Founder Principle-driven Enrichment (FPE), a method based on the population genetics "founder principle," to directly isolate rare mutant BACs, without any selectable marker, from liquid cultures via the polymerase chain reaction (PCR). Here, we provide a detailed description of FPE, including protocols for BAC recombineering and PCR screening. © 2017 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
- George T Lyozin
- Eccles Institute of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah.,University of Nebraska and Children's Hospital Medical Center, Omaha, Nebraska
| | - Yasuhiro Kosaka
- Eccles Institute of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah
| | - Gourab Bhattacharje
- Eccles Institute of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah
| | - H Joseph Yost
- Eccles Institute of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah
| | - Luca Brunelli
- Eccles Institute of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah.,Department of Pediatrics (Neonatology), The University of Utah School of Medicine, Salt Lake City, Utah
| |
Collapse
|
7
|
Hotta A, Yamanaka S. From Genomics to Gene Therapy: Induced Pluripotent Stem Cells Meet Genome Editing. Annu Rev Genet 2015; 49:47-70. [PMID: 26407033 DOI: 10.1146/annurev-genet-112414-054926] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The advent of induced pluripotent stem (iPS) cells has opened up numerous avenues of opportunity for cell therapy, including the initiation in September 2014 of the first human clinical trial to treat dry age-related macular degeneration. In parallel, advances in genome-editing technologies by site-specific nucleases have dramatically improved our ability to edit endogenous genomic sequences at targeted sites of interest. In fact, clinical trials have already begun to implement this technology to control HIV infection. Genome editing in iPS cells is a powerful tool and enables researchers to investigate the intricacies of the human genome in a dish. In the near future, the groundwork laid by such an approach may expand the possibilities of gene therapy for treating congenital disorders. In this review, we summarize the exciting progress being made in the utilization of genomic editing technologies in pluripotent stem cells and discuss remaining challenges toward gene therapy applications.
Collapse
Affiliation(s)
- Akitsu Hotta
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8501, Japan; .,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto 606-8501, Japan
| | - Shinya Yamanaka
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8501, Japan; .,Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Kyoto 606-8501, Japan.,Gladstone Institute of Cardiovascular Disease, San Francisco, California 94158
| |
Collapse
|
8
|
Kumar A, Lualdi M, Lyozin GT, Sharma P, Loncarek J, Fu XY, Kuehn MR. Nodal signaling from the visceral endoderm is required to maintain Nodal gene expression in the epiblast and drive DVE/AVE migration. Dev Biol 2014; 400:1-9. [PMID: 25536399 DOI: 10.1016/j.ydbio.2014.12.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 12/10/2014] [Accepted: 12/11/2014] [Indexed: 02/06/2023]
Abstract
In the early mouse embryo, a specialized population of extraembryonic visceral endoderm (VE) cells called the distal VE (DVE) arises at the tip of the egg cylinder stage embryo and then asymmetrically migrates to the prospective anterior, recruiting additional distal cells. Upon migration these cells, called the anterior VE (AVE), establish the anterior posterior (AP) axis by restricting gastrulation-inducing signals to the opposite pole. The Nodal-signaling pathway has been shown to have a critical role in the generation and migration of the DVE/AVE. The Nodal gene is expressed in both the VE and in the pluripotent epiblast, which gives rise to the germ layers. Previous findings have provided conflicting evidence as to the relative importance of Nodal signaling from the epiblast vs. VE for AP patterning. Here we show that conditional mutagenesis of the Nodal gene specifically within the VE leads to reduced Nodal expression levels in the epiblast and incomplete or failed DVE/AVE migration. These results support a required role for VE Nodal to maintain normal levels of expression in the epiblast, and suggest signaling from both VE and epiblast is important for DVE/AVE migration.
Collapse
Affiliation(s)
- Amit Kumar
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, United States
| | - Margaret Lualdi
- Laboratory Animal Sciences Program, SAIC-Frederick, Frederick, MD 21702, United States
| | - George T Lyozin
- Department of Pediatrics (Neonatology), The University of Utah, Salt Lake City, UT 84112, United States
| | - Prashant Sharma
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, United States
| | - Jadranka Loncarek
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, United States
| | - Xin-Yuan Fu
- Cancer Science Institute of Singapore, Singapore 117599, Singapore
| | - Michael R Kuehn
- Laboratory of Protein Dynamics and Signaling, Center for Cancer Research, National Cancer Institute, National Institutes of Health, United States.
| |
Collapse
|