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Li Z, Wang Y, Wang X, Niu S, Su Z, Wang F, Ni J, Gong Y, Rao B. A Fusion of Taq DNA Polymerase with the CL7 Protein from Escherichia coli Remarkably Improves DNA Amplification. Molecules 2024; 29:1145. [PMID: 38474657 DOI: 10.3390/molecules29051145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/11/2024] [Accepted: 01/26/2024] [Indexed: 03/14/2024] Open
Abstract
DNA polymerases are important enzymes that synthesize DNA molecules and therefore are critical to various scientific fields as essential components of in vitro DNA synthesis reactions, including PCR. Modern diagnostics, molecular biology, and genetic engineering require DNA polymerases with improved performance. This study aimed to obtain and characterize a new CL7-Taq fusion DNA polymerase, in which the DNA coding sequence of Taq DNA polymerase was fused with that of CL7, a variant of CE7 (Colicin E7 DNase) from Escherichia coli. The resulting novel recombinant open reading frame was cloned and expressed in E. coli. The recombinant CL7-Taq protein exhibited excellent thermostability, extension rate, sensitivity, and resistance to PCR inhibitors. Our results showed that the sensitivity of CL7-Taq DNA polymerase was 100-fold higher than that of wild-type Taq, which required a template concentration of at least 1.8 × 105 nM. Moreover, the extension rate of CL7-Taq was 4 kb/min, which remarkably exceeded the rate of Taq DNA polymerase (2 kb/min). Furthermore, the CL7 fusion protein showed increased resistance to inhibitors of DNA amplification, including lactoferrin, heparin, and blood. Single-cope human genomic targets were readily available from whole blood, and pretreatment to purify the template DNA was not required. Thus, this is a novel enzyme that improved the properties of Taq DNA polymerase, and thus may have wide application in molecular biology and diagnostics.
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Affiliation(s)
- Zhongchen Li
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China
| | - Yaping Wang
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China
| | - Xiangyi Wang
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China
| | - Shuhui Niu
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China
| | - Zhenlong Su
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China
| | - Fei Wang
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China
| | - Jing Ni
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China
| | - Yan Gong
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China
- Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Biopesticide Branch of Hubei Innovation Centre of Agricultural Science and Technology, Wuhan 430064, China
| | - Ben Rao
- State Key Laboratory of Biocatalysis and Enzyme, Engineering Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, Biology Faculty of Hubei University, Hubei University, Wuhan 430062, China
- Hubei Biopesticide Engineering Research Center, Hubei Academy of Agricultural Sciences, Biopesticide Branch of Hubei Innovation Centre of Agricultural Science and Technology, Wuhan 430064, China
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2
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Kuznetsova AA, Kuznetsov NA. Direct Enzyme Engineering of B Family DNA Polymerases for Biotechnological Approaches. Bioengineering (Basel) 2023; 10:1150. [PMID: 37892880 PMCID: PMC10604792 DOI: 10.3390/bioengineering10101150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/14/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
DNA-dependent DNA polymerases have been intensively studied for more than 60 years and underlie numerous biotechnological and diagnostic applications. In vitro, DNA polymerases are used for DNA manipulations, including cloning, PCR, site-directed mutagenesis, sequencing, and others. Understanding the mechanisms of action of DNA polymerases is important for the creation of new enzymes possessing improved or modified properties. This review is focused on archaeal family B DNA polymerases. These enzymes have high fidelity and thermal stability and are finding many applications in molecular biological methods. Nevertheless, the search for and construction of new DNA polymerases with altered properties is constantly underway, including enzymes for synthetic biology. This brief review describes advances in the development of family B DNA polymerases for PCR, synthesis of xeno-nucleic acids, and reverse transcription.
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Affiliation(s)
- Aleksandra A. Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad. Lavrentyeva, Novosibirsk 630090, Russia
| | - Nikita A. Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of Russian Academy of Sciences (SB RAS), 8 Prospekt Akad. Lavrentyeva, Novosibirsk 630090, Russia
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova Str., Novosibirsk 630090, Russia
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3
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Lee SJ, Park SY, Lee KH, Lee MW, Yu CY, Maeng J, Kim HD, Kim SW. Development of a Simple Direct and Hot-Start PCR Using Escherichia coli-Expressing Taq DNA Polymerase. Int J Mol Sci 2023; 24:11405. [PMID: 37511160 PMCID: PMC10379934 DOI: 10.3390/ijms241411405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/06/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Taq DNA polymerases have played an important role in molecular biology for several years and are frequently used for polymerase chain reaction (PCR); hence, there is an increasing interest in developing a convenient method for preparing Taq DNA polymerase for routine use in laboratories. We developed a method using Escherichia coli (E. coli) that expresses thermostable Taq DNA polymerase directly in the PCR without purification. The Taq gene was transformed into E. coli and expressed. After overnight incubation and washing, E. coli-expressing Taq DNA polymerase (EcoliTaq) was used as the DNA polymerase without purification. EcoliTaq showed activity comparable to that of commercial DNA polymerase and remained stable for 3 months. With a high-pH buffer containing 2% Tween 20 and 0.4 M trehalose, EcoliTaq facilitated direct PCR amplification from anticoagulated whole blood samples. EcoliTaq exhibited good performance in allele-specific PCR using both purified DNA and whole blood samples. Furthermore, it proved to be useful as a DNA polymerase in hot-start PCR by effectively minimizing non-specific amplification. We developed a simple and cost-effective direct and hot-start PCR method in which EcoliTaq was used directly as a PCR enzyme, thus eliminating the laborious and time-consuming steps of polymerase purification.
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Affiliation(s)
- Sun Ju Lee
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
| | - Sang-Yong Park
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
| | - Kwang-Ho Lee
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- Department of Laboratory Medicine, ASAN Medical Center, 88 Olympic-ro 43-gil, Songpa-gu, Seoul 05505, Republic of Korea
| | - Min-Woo Lee
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
| | - Chae-Yeon Yu
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- Graduate School of Particulate Matter Specialization, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
| | - Jaeyoung Maeng
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- Graduate School of Particulate Matter Specialization, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
| | - Hyeong-Dong Kim
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
| | - Suhng Wook Kim
- Department of Health and Safety Convergence Science, Graduate School, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
- Graduate School of Particulate Matter Specialization, Korea University, 145 Anam-ro, Seoul 02841, Republic of Korea
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4
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Ordóñez CD, Redrejo-Rodríguez M. DNA Polymerases for Whole Genome Amplification: Considerations and Future Directions. Int J Mol Sci 2023; 24:ijms24119331. [PMID: 37298280 DOI: 10.3390/ijms24119331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
In the same way that specialized DNA polymerases (DNAPs) replicate cellular and viral genomes, only a handful of dedicated proteins from various natural origins as well as engineered versions are appropriate for competent exponential amplification of whole genomes and metagenomes (WGA). Different applications have led to the development of diverse protocols, based on various DNAPs. Isothermal WGA is currently widely used due to the high performance of Φ29 DNA polymerase, but PCR-based methods are also available and can provide competent amplification of certain samples. Replication fidelity and processivity must be considered when selecting a suitable enzyme for WGA. However, other properties, such as thermostability, capacity to couple replication, and double helix unwinding, or the ability to maintain DNA replication opposite to damaged bases, are also very relevant for some applications. In this review, we provide an overview of the different properties of DNAPs widely used in WGA and discuss their limitations and future research directions.
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Affiliation(s)
- Carlos D Ordóñez
- CIC bioGUNE, Bizkaia Science and Technology Park, Building 800, 48160 Derio, Spain
| | - Modesto Redrejo-Rodríguez
- Department of Biochemistry, Universidad Autónoma de Madrid and Instituto de Investigaciones Biomédicas "Alberto Sols", CSIC-UAM, 28029 Madrid, Spain
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5
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Farasati Far B, Safaei M, Mokhtari F, Fallahi MS, Naimi-Jamal MR. Fundamental concepts of protein therapeutics and spacing in oncology: an updated comprehensive review. Med Oncol 2023; 40:166. [PMID: 37147486 DOI: 10.1007/s12032-023-02026-5] [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: 01/31/2023] [Accepted: 04/06/2023] [Indexed: 05/07/2023]
Abstract
Current treatment regimens in cancer cases cause significant side effects and cannot effectively eradicate the advanced disease. Hence, much effort has been expended over the past years to understand how cancer grows and responds to therapies. Meanwhile, proteins as a type of biopolymers have been under commercial development for over three decades and have been proven to improve the healthcare system as effective medicines for treating many types of progressive disease, such as cancer. Following approving the first recombinant protein therapeutics by FDA (Humulin), there have been a revolution for drawing attention toward protein-based therapeutics (PTs). Since then, the ability to tailor proteins with ideal pharmacokinetics has provided the pharmaceutical industry with an important noble path to discuss the clinical potential of proteins in oncology research. Unlike traditional chemotherapy molecules, PTs actively target cancerous cells by binding to their surface receptors and the other biomarkers particularly associated with tumorous or healthy tissue. This review analyzes the potential and limitations of protein therapeutics (PTs) in the treatment of cancer as well as highlighting the evolving strategies by addressing all possible factors, including pharmacology profile and targeted therapy approaches. This review provides a comprehensive overview of the current state of PTs in oncology, including their pharmacology profile, targeted therapy approaches, and prospects. The reviewed data show that several current and future challenges remain to make PTs a promising and effective anticancer drug, such as safety, immunogenicity, protein stability/degradation, and protein-adjuvant interactions.
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Affiliation(s)
- Bahareh Farasati Far
- Research Laboratory of Green Organic Synthesis and Polymers, Department of Chemistry, Iran University of Science and Technology, Narmak, Tehran, Iran
| | - Maryam Safaei
- Department of Pharmacology, Faculty of Pharmacy, Eastern Mediterranean University, Via Mersin 10, TR. North Cyprus, Famagusta, Turkey
| | - Fatemeh Mokhtari
- Department of Chemistry, Faculty of Basic Science, Azarbaijan Shahid Madani (ASMU), Tabriz, 53751-71379, Iran
| | | | - Mohammad Reza Naimi-Jamal
- Research Laboratory of Green Organic Synthesis and Polymers, Department of Chemistry, Iran University of Science and Technology, Narmak, Tehran, Iran.
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Ahmad S, Ali SF, Iftikhar S, Rashid N. Engineering a DNA polymerase from Pyrobaculum calidifontis for improved activity, processivity and extension rate. Int J Biol Macromol 2023; 233:123545. [PMID: 36740112 DOI: 10.1016/j.ijbiomac.2023.123545] [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: 10/12/2022] [Revised: 01/20/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
Positively charged amino acids in the DNA polymerase domain are important for interaction with DNA. Two potential residues in the palm domain of Pca-Pol, a DNA polymerase from Pyrobaculum calidifontis, were identified and mutated to arginine in order to improve the properties of this enzyme. The mutant proteins were heterologously produced in Escherichia coli. Biochemical characterization revealed that there was no significant difference in pH, metal ion, buffer preferences, 3' - 5' exonuclease activity and error rate of the wild-type and the mutant enzymes. However, the specific activity, processivity and extension rate of the mutant enzymes increased significantly. Specific activity of one of the mutants (G522R-E555R) was nearly 9-fold higher than that of the wild-type enzyme. These properties make G522R-E555R mutant enzyme a potential candidate for commercial applications.
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Affiliation(s)
- Shazeel Ahmad
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Syed Farhat Ali
- KAM-School of Life Sciences, Forman Christian College (A Chartered University), Ferozepur Road, Lahore 54600, Pakistan
| | - Saima Iftikhar
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan
| | - Naeem Rashid
- School of Biological Sciences, University of the Punjab, Quaid-e-Azam Campus, Lahore 54590, Pakistan.
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7
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Sarlak Z, Shojaee-Aliabadi S, Rezvani N, Hosseini H, Rouhi M, Dastafkan Z. Development and validation of TaqMan real-time PCR assays for quantification of chicken adulteration in hamburgers. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2021.104302] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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8
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PCR enhancers: Types, mechanisms, and applications in long-range PCR. Biochimie 2022; 197:130-143. [DOI: 10.1016/j.biochi.2022.02.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 02/06/2022] [Accepted: 02/24/2022] [Indexed: 12/21/2022]
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9
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Hafez M, Abdelmagid A, Aboukhaddour R, Adam LR, Daayf F. Fusarium Root Rot Complex in Soybean: Molecular Characterization, Trichothecene Formation, and Cross-Pathogenicity. PHYTOPATHOLOGY 2021; 111:2287-2302. [PMID: 33938238 DOI: 10.1094/phyto-03-21-0083-r] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Soybean is threatened by many pathogens that negatively affect this crop's yield and quality, such as various Fusarium species that cause wilting and root rot diseases. Fusarium root rot (FRR) in soybean can be caused by F. graminearum and other Fusarium spp. that are associated with Fusarium head blight (FHB) in cereals. Therefore, it was important to inquire whether Fusarium pathogens from soybean can cause disease in wheat and vice versa. Here, we investigated the FRR complex in Manitoba (Canada) from symptomatic plants, using both culture- and molecular-based methods. We developed a molecular diagnostic toolkit to detect and differentiate between several Fusarium spp. involved in FHB and FRR, then we evaluated cross-pathogenicity of selected Fusarium isolates collected from soybean and wheat, and the results indicate that isolates recovered from one host can infect the other host. Trichothecene production by selected Fusarium spp. was also analyzed chemically via liquid chromatography mass spectrometry in both soybean (root) and wheat (spike) tissues. Trichothecenes were also analyzed in soybean seeds from plants with FRR to check the potentiality of trichothecene translocation from infected roots to the seeds. All of the tested Fusarium isolates were capable of producing trichothecenes in wheat spikes and soybean roots, but no trichothecenes were detected in soybean seeds. This study provided evidence, for the first time, that trichothecenes were produced by several Fusarium spp. (F. cerealis, F. culmorum, and F. sporotrichioides) during FRR development in soybean.
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Affiliation(s)
- Mohamed Hafez
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, R3T2N2, Canada
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Center, Lethbridge, Alberta, Canada
- Department of Botany and Microbiology, Faculty of Science, Suez University, Suez, Egypt
| | - Ahmed Abdelmagid
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, R3T2N2, Canada
- Department of Plant Pathology, Assiut University, Assiut, 71515, Egypt
| | - Reem Aboukhaddour
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Center, Lethbridge, Alberta, Canada
| | - Lorne R Adam
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, R3T2N2, Canada
| | - Fouad Daayf
- Department of Plant Science, University of Manitoba, Winnipeg, Manitoba, R3T2N2, Canada
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Pavelquesi SLS, de Oliveira Ferreira ACA, Rodrigues ARM, de Souza Silva CM, Orsi DC, da Silva ICR. Presence of Tetracycline and Sulfonamide Resistance Genes in Salmonella spp.: Literature Review. Antibiotics (Basel) 2021; 10:antibiotics10111314. [PMID: 34827252 PMCID: PMC8615168 DOI: 10.3390/antibiotics10111314] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 12/19/2022] Open
Abstract
Tetracyclines and sulfonamides are broad-spectrum antibacterial agents which have been used to treat bacterial infections for over half a century. The widespread use of tetracyclines and sulfonamides led to the emergence of resistance in a diverse group of bacteria. This resistance can be studied by searching for resistance genes present in the bacteria responsible for different resistance mechanisms. Salmonella is one of the leading bacteria causing foodborne diseases worldwide, and its resistance to tetracyclines and sulfonamides has been widely reported. The literature review searched the Virtual Health Library for articles with specific data in the studied samples: the resistance genes found, the primers used in PCR, and the thermocycler conditions. The results revealed that Salmonella presented high rates of resistance to tetracycline and sulfonamide, and the most frequent samples used to isolate Salmonella were poultry and pork. The tetracycline resistance genes most frequently detected from Salmonella spp. were tetA followed by tetB. The gene sul1 followed by sul2 were the most frequently sulfonamide resistance genes present in Salmonella. These genes are associated with plasmids, transposons, or both, and are often conjugative, highlighting the transference potential of these genes to other bacteria, environments, animals, and humans.
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11
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Use and Misuse of C q in qPCR Data Analysis and Reporting. Life (Basel) 2021; 11:life11060496. [PMID: 34072308 PMCID: PMC8229287 DOI: 10.3390/life11060496] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 02/06/2023] Open
Abstract
In the analysis of quantitative PCR (qPCR) data, the quantification cycle (Cq) indicates the position of the amplification curve with respect to the cycle axis. Because Cq is directly related to the starting concentration of the target, and the difference in Cq values is related to the starting concentration ratio, the only results of qPCR analysis reported are often Cq, ΔCq or ΔΔCq values. However, reporting of Cq values ignores the fact that Cq values may differ between runs and machines, and, therefore, cannot be compared between laboratories. Moreover, Cq values are highly dependent on the PCR efficiency, which differs between assays and may differ between samples. Interpreting reported Cq values, assuming a 100% efficient PCR, may lead to assumed gene expression ratios that are 100-fold off. This review describes how differences in quantification threshold setting, PCR efficiency, starting material, PCR artefacts, pipetting errors and sampling variation are at the origin of differences and variability in Cq values and discusses the limits to the interpretation of observed Cq values. These issues can be avoided by calculating efficiency-corrected starting concentrations per reaction. The reporting of gene expression ratios and fold difference between treatments can then easily be based on these starting concentrations.
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12
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Lee NE, Ha DI, Ko JH, Kim YS. One-step genotyping method in CRISPR based on short inner primer-assisted, tetra primer-paired amplifications. Mol Cell Probes 2021; 55:101675. [PMID: 33245992 DOI: 10.1016/j.mcp.2020.101675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 11/12/2020] [Accepted: 11/20/2020] [Indexed: 11/26/2022]
Abstract
Base editors and prime editors induce precise DNA modifications over one or several nucleotides in eukaryotic cells. The T7E1 assay has been widely adopted for the assessment of genome editing, but it has several limitations in the applications for prime editing and base editing due to low sensitivity, inaccuracy and additional disadvantages. Here, we propose a short inner primer-assisted, tetra primer-paired amplification (SIPATA) method as an alternative to T7E1 analysis. SIPATA is a PCR-based method in which two long outer and two short (15 nt) inner primers are used for the amplification of a specific genotype in the presence of Hot start-Taq. One of the inner primers carries a 3'-terminally wild-type nucleotide sequence, and the other carries a post-editing sequence. Under optimized conditions, SIPATA enabled sensitive and accurate genotyping of single-nucleotide conversions by base editors and prime editors. Furthermore, SIPATA could be applied to trace low levels of DNA modifications achieved by HDR-mediated gene correction or chimerism during the generation of model animals. Multiplexed genotyping was also possible without compromising those multifaceted analytical advantages of SIPATA. Our findings demonstrate that SIPATA offers a robust, fast and sensitive genotyping platform for single-nucleotide variations in a variety of CRISPR applications.
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Affiliation(s)
- Nan-Ee Lee
- Genome Editing Research Center, KRIBB, Daejeon (34141), Republic of Korea; Department of Bio-molecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon (34113), Republic of Korea
| | - Dae-In Ha
- Genome Editing Research Center, KRIBB, Daejeon (34141), Republic of Korea; Department of Bio-molecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon (34113), Republic of Korea
| | - Jeong-Heon Ko
- Genome Editing Research Center, KRIBB, Daejeon (34141), Republic of Korea; Department of Bio-molecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon (34113), Republic of Korea
| | - Yong-Sam Kim
- Genome Editing Research Center, KRIBB, Daejeon (34141), Republic of Korea; Department of Bio-molecular Science, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon (34113), Republic of Korea; GenKOre, Daejeon (34141), Republic of Korea.
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13
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Saghatelyan A, Panosyan H, Trchounian A, Birkeland NK. Characteristics of DNA polymerase I from an extreme thermophile, Thermus scotoductus strain K1. Microbiologyopen 2021; 10:e1149. [PMID: 33415847 PMCID: PMC7884927 DOI: 10.1002/mbo3.1149] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/30/2020] [Accepted: 12/07/2020] [Indexed: 01/04/2023] Open
Abstract
Several native and engineered heat‐stable DNA polymerases from a variety of sources are used as powerful tools in different molecular techniques, including polymerase chain reaction, medical diagnostics, DNA sequencing, biological diversity assessments, and in vitro mutagenesis. The DNA polymerase from the extreme thermophile, Thermus scotoductus strain K1, (TsK1) was expressed in Escherichia coli, purified, and characterized. This enzyme belongs to a distinct phylogenetic clade, different from the commonly used DNA polymerase I enzymes, including those from Thermus aquaticus and Thermus thermophilus. The enzyme demonstrated an optimal temperature and pH value of 72–74°C and 9.0, respectively, and could efficiently amplify 2.5 kb DNA products. TsK1 DNA polymerase did not require additional K+ ions but it did need Mg2+ at 3–5 mM for optimal activity. It was stable for at least 1 h at 80°C, and its half‐life at 88 and 95°C was 30 and 15 min, respectively. Analysis of the mutation frequency in the amplified products demonstrated that the base insertion fidelity for this enzyme was significantly better than that of Taq DNA polymerase. These results suggest that TsK1 DNA polymerase could be useful in various molecular applications, including high‐temperature DNA polymerization.
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Affiliation(s)
- Ani Saghatelyan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, Yerevan, Armenia.,Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Hovik Panosyan
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, Yerevan, Armenia
| | - Armen Trchounian
- Department of Biochemistry, Microbiology and Biotechnology, Yerevan State University, Yerevan, Armenia
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14
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Engineered viral DNA polymerase with enhanced DNA amplification capacity: a proof-of-concept of isothermal amplification of damaged DNA. Sci Rep 2020; 10:15046. [PMID: 32929102 PMCID: PMC7490695 DOI: 10.1038/s41598-020-71773-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 08/20/2020] [Indexed: 11/24/2022] Open
Abstract
The development of whole genome amplification (WGA) and related methods, coupled with the dramatic growth of sequencing capacities, has changed the paradigm of genomic and genetic analyses. This has led to a continual requirement of improved DNA amplification protocols and the elaboration of new tailored methods. As key elements in WGA, identification and engineering of novel, faithful and processive DNA polymerases is a driving force in the field. We have engineered the B-family DNA polymerase of virus Bam35 with a C-terminal fusion of DNA-binding motifs. The new protein, named B35-HhH, shows faithful DNA replication in the presence of magnesium or an optimised combination of magnesium and manganese divalent cofactors, which enhances the replication of damaged DNA substrates. Overall, the newly generated variant displays improved amplification performance, sensitivity, translesion synthesis and resistance to salt, which are of great interest for several applications of isothermal DNA amplification. Further, rolling-circle amplification of abasic site-containing minicircles provides a proof-of-concept for using B35-HhH for processive amplification of damaged DNA samples.
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Understanding the Effect of Multiple Domain Deletion in DNA Polymerase I from Geobacillus Sp. Strain SK72. Catalysts 2020. [DOI: 10.3390/catal10080936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The molecular structure of DNA polymerase I or family A polymerases is made up of three major domains that consist of a single polymerase domain with two extra exonuclease domains. When the N-terminal was deleted, the enzyme was still able to perform basic polymerase activity with additional traits that used isothermal amplification. However, the 3′-5′ exonuclease domain that carries a proofreading activity was disabled. Yet, the structure remained attached to the 5′-3′ polymerization domain without affecting its ability. The purpose of this non-functional domain still remains scarce. It either gives negative effects or provides structural support to the DNA polymerase. Here, we compared the effect of deleting each domain against the polymerase activity. The recombinant wild type and its variants were successfully purified and characterized. Interestingly, SK72-Exo (a large fragment excluding the 5′-3′ exonuclease domain) exhibited better catalytic activity than the native SK72 (with all three domains) at similar optimum temperature and pH profile, and it showed longer stability at 70 °C. Meanwhile, SK72-Exo2 (polymerization domain without both the 5′-3′ and 3′-5′ exonuclease domain) displayed the lowest activity with an optimum at 40 °C and favored a more neutral environment. It was also the least stable among the variants, with almost no activity at 50 °C for the first 10 min. In conclusion, cutting both exonuclease domains in DNA polymerase I has a detrimental effect on the polymerization activity and structural stability.
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Ezzedine JA, Chardon C, Jacquet S. New 16S rRNA primers to uncover Bdellovibrio and like organisms diversity and abundance. J Microbiol Methods 2020; 175:105996. [PMID: 32598974 DOI: 10.1016/j.mimet.2020.105996] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/24/2020] [Accepted: 06/24/2020] [Indexed: 11/29/2022]
Abstract
Appropriate use and specific primers are important in assessing the diversity and abundance of microbial groups of interest. Bdellovibrio and like organisms (BALOs), that refer to obligate Gram-negative bacterial predators of other Gram-negative bacteria, evolved in terms of taxonomy and classification over the past two decades. Hence, some former primers have become inadequate while others are yet to be designed, for both PCR (especially with the advent of NGS) and qPCR approaches. Thus, to study BALOs' abundance and diversity in a variety of aquatic ecosystems, we designed in silico specific primer sets for each BALO genera and tested them in vitro on a variety of cultures and environmental samples. Also, we performed Sanger and Nano Miseq sequencing to reveal the exact degree of specificity of the most promising primers set. Here we report our success in designing specific primers for some BALOs genera, i.e. Bdellovibrio (PCR), Bacteriovorax (qPCR), Peredibacter (PCR).
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Affiliation(s)
- Jade A Ezzedine
- Université Savoie Mont-Blanc, INRAE, UMR CARRTEL, Thonon-les-Bains, France
| | - Cécile Chardon
- Université Savoie Mont-Blanc, INRAE, UMR CARRTEL, Thonon-les-Bains, France
| | - Stéphan Jacquet
- Université Savoie Mont-Blanc, INRAE, UMR CARRTEL, Thonon-les-Bains, France.
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Thongjued K, Chotigeat W, Bumrungsri S, Thanakiatkrai P, Kitpipit T. A new cost-effective and fast direct PCR protocol for insects based on PBS buffer. Mol Ecol Resour 2019; 19:691-701. [PMID: 30758899 DOI: 10.1111/1755-0998.13005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 02/06/2019] [Accepted: 02/08/2019] [Indexed: 01/26/2023]
Abstract
Insect DNA barcoding is a species identification technique used in biodiversity assessment and ecological studies. However, DNA extraction can result in the loss of up to 70% of DNA. Recent research has reported that direct PCR can overcome this issue. However, the success rates could still be improved, and tissues used for direct PCR could not be reused for further genetic studies. Here, we developed a direct PCR workflow that incorporates a 2-min sample preparation in PBS-buffer step for fast and effective universal insect species identification. The developed protocol achieved 100% success rates for amplification in six orders: Mantodea, Phasmatodea, Neuroptera, Odonata, Blattodea and Orthoptera. High and moderate success rates were obtained for five other species: Lepidoptera (97.3%), Coleoptera (93.8%), Diptera (90.5%), Hemiptera (81.8%) and Hymenoptera (75.0%). High-quality sequencing data were also obtained from these amplifiable products, allowing confidence in species identification. The method was sensitive down to 1/4th of a 1-mm fragment of leg or body and its success rates with oven-dried, ethanol-preserved, food, bat guano and museum specimens were 100%, 98.6%, 90.0%, 84.0% and 30.0%, respectively. In addition, the pre-PCR solution (PBS with insect tissues) could be used for further DNA extraction if needed. The workflow will be beneficial in the fields of insect taxonomy and ecological studies due to its low cost, simplicity and applicability to highly degraded specimens.
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Affiliation(s)
- Kantima Thongjued
- Department of Molecular Biotechnology and Bioinformatics, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Wilaiwan Chotigeat
- Department of Molecular Biotechnology and Bioinformatics, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.,Center for Genomics and Bioinformatics Research, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Sara Bumrungsri
- Department of Biology, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Phuvadol Thanakiatkrai
- Forensic Science Program, Department of Applied Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
| | - Thitika Kitpipit
- Forensic Science Program, Department of Applied Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand
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Sankar PS, Citartan M, Siti AA, Skryabin BV, Rozhdestvensky TS, Khor GH, Tang TH. A simple method for in-house Pfu DNA polymerase purification for high-fidelity PCR amplification. IRANIAN JOURNAL OF MICROBIOLOGY 2019; 11:181-186. [PMID: 31341574 PMCID: PMC6635313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
BACKGROUND AND OBJECTIVES Pfu DNA polymerase is an enzyme that exhibits the lowest error rate in the 3' to 5' exonuclease (proofreading) activity during DNA synthesis in Polymerase Chain Reactions (PCRs). This study was aimed to express and purify Pfu DNA polymerase in a bacterial expression system under a simple purification method. MATERIALS AND METHODS Pfu polymerase gene sequence, derived from Pyrocuccus furiosus (Pfu) genomic DNA, was cloned and overexpressed in E. coli BL21 (DE3) pLysS. Upon overexpression, bacterial lysate containing the Pfu DNA polymerase was heated at 94°C for 5 minutes. Pfu DNA polymerase having high thermal stability was retained while the other bacterial proteins were denatured. The resulting thermo stable Pfu DNA polymerase was separated from the other debris of the denatured proteins by simple centrifugation. RESULTS The enzymatic activity of the resulting Pfu DNA polymerase was estimated by comparing with the commercial Pfu DNA Polymerases. An estimated 50000 units of functional Pfu DNA polymerase was produced from a 400 ml culture. CONCLUSION The in-house produced Pfu DNA Polymerase could be used for routine amplification that requires high-fidelity such as cloning and DNA sequencing.
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Affiliation(s)
- Prabu Siva Sankar
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, Kepala Batas, Penang, Malaysia
| | - Marimuthu Citartan
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, Kepala Batas, Penang, Malaysia,Corresponding author: Marimuthu Citartan, Ph.D, Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, Kepala Batas, Penang, Malaysia. Tel: +604 5622257,
| | - Aminah Ahmed Siti
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, Kepala Batas, Penang, Malaysia
| | - Boris V. Skryabin
- Faculty of Medical (TRAM), University of Muenster, Muenster, Germany
| | | | - Goot Heah Khor
- Centre of Preclinical Science Studies, Faculty of Dentistry, Universiti Teknologi MARA, Sungai Buluh Campus, Selangor, Malaysia
| | - Thean Hock Tang
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, Kepala Batas, Penang, Malaysia
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Olszewski M, Śpibida M, Bilek M, Krawczyk B. Fusion of Taq DNA polymerase with single-stranded DNA binding-like protein of Nanoarchaeum equitans-Expression and characterization. PLoS One 2017; 12:e0184162. [PMID: 28863186 PMCID: PMC5581180 DOI: 10.1371/journal.pone.0184162] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 08/19/2017] [Indexed: 11/25/2022] Open
Abstract
DNA polymerases are present in all organisms and are important enzymes that synthesise DNA molecules. They are used in various fields of science, predominantly as essential components for in vitro DNA syntheses, known as PCR. Modern diagnostics, molecular biology and genetic engineering need DNA polymerases which demonstrate improved performance. This study was aimed at obtaining a new NeqSSB-TaqS fusion DNA polymerase from the Taq DNA Stoffel domain and a single-stranded DNA binding-like protein of Nanoarchaeum equitans in order to significantly improve the properties of DNA polymerase. The DNA coding sequence of Taq Stoffel DNA polymerase and the nonspecific DNA-binding protein of Nanoarchaeum equitans (NeqSSB-like protein) were fused. A novel recombinant gene was obtained which was cloned into the pET-30 Ek/LIC vector and introduced into E. coli for expression. The recombinant enzyme was purified and its enzymatic properties including DNA polymerase activity, PCR amplification rate, thermostability, processivity and resistance to inhibitors, were tested. The yield of the target protein reached approximately 18 mg/l after 24 h of the IPTG induction. The specific activity of the polymerase was 2200 U/mg. The recombinant NeqSSB-TaqS exhibited a much higher extension rate (1000 bp template in 20 s), processivity (19 nt), thermostability (half-life 35 min at 95°C) and higher tolerance to PCR inhibitors (0.3–1.25% of whole blood, 0.84–13.5 μg of lactoferrin and 4.7–150 ng of heparin) than Taq Stoffel DNA polymerase. Furthermore, our studies show that NeqSSB-TaqS DNA polymerase has a high level of flexibility in relation to Mg2+ ions (from 1 to 5 mM) and KCl or (NH4)2SO4 salts (more than 60 mM and 40 mM, respectively). Using NeqSSB-TaqS DNA polymerase instead of the Taq DNA polymerase could be a better choice in many PCR applications.
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Affiliation(s)
- Marcin Olszewski
- Gdańsk University of Technology, Department of Molecular Biotechnology and Microbiology, ul. G. Narutowicza 11/12, Gdańsk, Poland
| | - Marta Śpibida
- Gdańsk University of Technology, Department of Molecular Biotechnology and Microbiology, ul. G. Narutowicza 11/12, Gdańsk, Poland
| | - Maciej Bilek
- Department of Food and Agriculture Production Engineering, University of Rzeszów, ul. Zelwerowicza 4, Rzeszów, Poland
| | - Beata Krawczyk
- Gdańsk University of Technology, Department of Molecular Biotechnology and Microbiology, ul. G. Narutowicza 11/12, Gdańsk, Poland
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