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Zhang F, Liu ZY, Liu S, Zhang WG, Wang BB, Li CL, Xu JZ. Rapid screening of point mutations by mismatch amplification mutation assay PCR. Appl Microbiol Biotechnol 2024; 108:190. [PMID: 38305911 PMCID: PMC10837254 DOI: 10.1007/s00253-024-13036-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 08/18/2023] [Accepted: 01/25/2024] [Indexed: 02/03/2024]
Abstract
Metabolic engineering frequently makes use of point mutation and saturation mutation library creation. At present, sequencing is the only reliable and direct technique to detect point mutation and screen saturation mutation library. In this study, mismatch amplification mutation assay (MAMA) PCR was used to detect point mutation and screen saturation mutation library. In order to fine-tune the expression of odhA encoding 2-oxoglutarate dehydrogenase E1 component, a saturating mutant library of the RBS of odhA was created in Corynebacterium glutamicum P12 based on the CRISPR-Cas2a genome editing system, which increased the L-proline production by 81.3%. MAMA PCR was used to filter out 42% of the non-mutant transformants in the mutant library, which effectively reduced the workload of the subsequent fermentation test and the number of sequenced samples. The rapid and sensitive MAMA-PCR method established in this study provides a general strategy for detecting point mutations and improving the efficiency of mutation library screening. KEY POINTS: • MAMA PCR was optimized and developed to detect point mutation. • MAMA PCR greatly improves the screening efficiency of point mutation. • Attenuation of odhA expression in P12 effectively improves proline production.
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Affiliation(s)
- Feng Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
| | - Zhen Yang Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
| | - Shuai Liu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
| | - Wei Guo Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China.
| | - Bing Bing Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
| | - Chang Lon Li
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
| | - Jian Zhong Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, 214122, People's Republic of China
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Pavlova LE, Timina MF, Agumava AA, Panchenko AV. Genotyping of Macaque Population on the Brain-Derived Neurotrophic Factor Gene Polymorphism by Mismatch Amplification Mutation Assay (MAMA)-PCR. Bull Exp Biol Med 2023; 175:388-392. [PMID: 37566252 DOI: 10.1007/s10517-023-05873-4] [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: 12/13/2022] [Indexed: 08/12/2023]
Abstract
Human rs6265 (196G>A) polymorphism in the BDNF gene is associated with many clinically significant phenotypic manifestations. Rhesus monkey (Macaca mulatta) has a functionally significant rs309950446 ( 136G>A) polymorphism. To determine this polymorphism in macaques, we used mismatch amplification mutation assay (MAMA)-PCR method with non-complementary nucleotide to the template chain at the 3rd position from the 3'-end of the allele-specific primers (mismatch primers), which allowed the best discrimination of the alleles. Genotyping of male rhesus monkeys (n=178) and cynomolgus monkeys (Macaca fascicularis) (n=90) was carried out. The A/A, G/G, and G/A genotypes were found in 16, 34, and 50% rhesus macaques, respectively. In the cynomolgus macaques, the mutant polymorphic allele was not detected. The study results allow considering rhesus macaques as a potential biological model for assessment of the gen-environment interaction of the BDNF gene polymorphism.
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Affiliation(s)
- L E Pavlova
- Research Institute of Medical Primatology, Sochi, Russia.
| | - M F Timina
- Research Institute of Medical Primatology, Sochi, Russia
| | - A A Agumava
- Research Institute of Medical Primatology, Sochi, Russia
| | - A V Panchenko
- Research Institute of Medical Primatology, Sochi, Russia
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3
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Ota Y, Okada R, Takahashi H, Saito R. A mismatch amplification mutation assay for specific detection of ciprofloxacin-resistant Neisseria meningitidis. J Infect Chemother 2023; 29:562-564. [PMID: 36758676 DOI: 10.1016/j.jiac.2023.02.004] [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: 01/06/2023] [Revised: 02/01/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023]
Abstract
Meningococcal chemoprophylaxis for people in close contact with patients with invasive meningococcal disease (IMD) is necessary for preventing the spread of Neisseria meningitidis. Ciprofloxacin (CIP) is commonly used to treat IMD. However, CIP-resistant N. meningitidis isolates have rapidly evolved worldwide; therefore, rapid and accurate detection of CIP-resistant N. meningitidis is essential. We developed a mismatch amplification mutation assay for identifying gyrA substitutions T91I and D95Y, associated with reduced CIP susceptibility, using two primer sets to detect these variants. Comparison with gyrA sequencing data showed complete congruency. This method enables reliable detection of CIP-resistant N. meningitidis, thus leading to efficient management and control of IMD infections.
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Affiliation(s)
- Yusuke Ota
- Department of Molecular Microbiology, Graduate School of Medicine and Dental Science, Tokyo Medical and Dental University, Tokyo, Japan
| | - Reina Okada
- Department of Molecular Microbiology, Graduate School of Medicine and Dental Science, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hideyuki Takahashi
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ryoichi Saito
- Department of Molecular Microbiology, Graduate School of Medicine and Dental Science, Tokyo Medical and Dental University, Tokyo, Japan.
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Negrón DA, Kang J, Mitchell S, Holland MY, Wist S, Voss J, Brinkac L, Jennings K, Guertin S, Goodwin BG, Sozhamannan S. Impact of SARS-CoV-2 Mutations on PCR Assay Sequence Alignment. Front Public Health 2022; 10:889973. [PMID: 35570946 PMCID: PMC9096222 DOI: 10.3389/fpubh.2022.889973] [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: 03/04/2022] [Accepted: 04/05/2022] [Indexed: 11/28/2022] Open
Abstract
Real-time reverse transcription polymerase chain reaction (RT-PCR) assays are the most widely used molecular tests for the detection of SARS-CoV-2 and diagnosis of COVID-19 in clinical samples. PCR assays target unique genomic RNA regions to identify SARS-CoV-2 with high sensitivity and specificity. In general, assay development incorporates the whole genome sequences available at design time to be inclusive of all target species and exclusive of near neighbors. However, rapid accumulation of mutations in viral genomes during sustained growth in the population can result in signature erosion and assay failures, creating situational blind spots during a pandemic. In this study, we analyzed the signatures of 43 PCR assays distributed across the genome against over 1.6 million SARS-CoV-2 sequences. We present evidence of significant signature erosion emerging in just two assays due to mutations, while adequate sequence identity was preserved in the other 41 assays. Failure of more than one assay against a given variant sequence was rare and mostly occurred in the two assays noted to have signature erosion. Assays tended to be designed in regions with statistically higher mutations rates. in silico analyses over time can provide insights into mutation trends and alert users to the emergence of novel variants that are present in the population at low proportions before they become dominant. Such routine assessment can also potentially highlight false negatives in test samples that may be indicative of mutations having functional consequences in the form of vaccine and therapeutic failures. This study highlights the importance of whole genome sequencing and expanded real-time monitoring of diagnostic PCR assays during a pandemic.
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Affiliation(s)
| | - June Kang
- Noblis, Inc., Reston, VA, United States
| | | | | | | | - Jameson Voss
- Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), Joint Project Lead for CBRND Enabling Biotechnologies (JPL CBRND EB), Frederick, MD, United States
| | | | | | | | - Bruce G Goodwin
- Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), Joint Project Lead for CBRND Enabling Biotechnologies (JPL CBRND EB), Frederick, MD, United States
| | - Shanmuga Sozhamannan
- Joint Program Executive Office for Chemical, Biological, Radiological and Nuclear Defense (JPEO-CBRND), Joint Project Lead for CBRND Enabling Biotechnologies (JPL CBRND EB), Frederick, MD, United States.,Logistics Management Institute, Tysons, VA, United States
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Rusu A, Lungu IA, Moldovan OL, Tanase C, Hancu G. Structural Characterization of the Millennial Antibacterial (Fluoro)Quinolones-Shaping the Fifth Generation. Pharmaceutics 2021; 13:pharmaceutics13081289. [PMID: 34452252 PMCID: PMC8399897 DOI: 10.3390/pharmaceutics13081289] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/12/2021] [Accepted: 08/14/2021] [Indexed: 12/12/2022] Open
Abstract
The evolution of the class of antibacterial quinolones includes the introduction in therapy of highly successful compounds. Although many representatives were withdrawn due to severe adverse reactions, a few representatives have proven their therapeutical value over time. The classification of antibacterial quinolones into generations is a valuable tool for physicians, pharmacists, and researchers. In addition, the transition from one generation to another has brought new representatives with improved properties. In the last two decades, several representatives of antibacterial quinolones received approval for therapy. This review sets out to chronologically outline the group of approved antibacterial quinolones since 2000. Special attention is given to eight representatives: besifloxacin, delafoxacin, finafloxacin, lascufloxacin, nadifloxacin and levonadifloxacin, nemonoxacin, and zabofloxacin. These compounds have been characterized regarding physicochemical properties, formulations, antibacterial activity spectrum and advantageous structural characteristics related to antibacterial efficiency. At present these new compounds (with the exception of nadifloxacin) are reported differently, most often in the fourth generation and less frequently in a new generation (the fifth). Although these new compounds' mechanism does not contain essential new elements, the question of shaping a new generation (the fifth) arises, based on higher potency and broad spectrum of activity, including resistant bacterial strains. The functional groups that ensured the biological activity, good pharmacokinetic properties and a safety profile were highlighted. In addition, these new representatives have a low risk of determining bacterial resistance. Several positive aspects are added to the fourth fluoroquinolones generation, characteristics that can be the basis of the fifth generation. Antibacterial quinolones class continues to acquire new compounds with antibacterial potential, among other effects. Numerous derivatives, hybrids or conjugates are currently in various stages of research.
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Affiliation(s)
- Aura Rusu
- Pharmaceutical and Therapeutical Chemistry Department, Faculty of Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Targu Mures, 540142 Targu Mures, Romania; (A.R.); (G.H.)
| | - Ioana-Andreea Lungu
- The Doctoral School of Medicine and Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Targu Mures, 540142 Targu Mures, Romania; (I.-A.L.); (O.-L.M.)
| | - Octavia-Laura Moldovan
- The Doctoral School of Medicine and Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Targu Mures, 540142 Targu Mures, Romania; (I.-A.L.); (O.-L.M.)
| | - Corneliu Tanase
- Pharmaceutical Botany Department, Faculty of Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Targu Mures, 540142 Targu Mures, Romania
- Correspondence: ; Tel.: +40-744-215-543
| | - Gabriel Hancu
- Pharmaceutical and Therapeutical Chemistry Department, Faculty of Pharmacy, George Emil Palade University of Medicine, Pharmacy, Science, and Technology of Targu Mures, 540142 Targu Mures, Romania; (A.R.); (G.H.)
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Lacouture S, Okura M, Takamatsu D, Corsaut L, Gottschalk M. Development of a mismatch amplification mutation assay to correctly serotype isolates of Streptococcus suis serotypes 1, 2, 1/2, and 14. J Vet Diagn Invest 2020; 32:490-494. [PMID: 32306861 DOI: 10.1177/1040638720915869] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Streptococcus suis is one of the most important bacterial swine pathogens worldwide and is an emerging pathogen in humans. There are 29 serotypes, and serotyping, which is based on the antigenicity of the capsular polysaccharide (CPS) or on its coding genes, is often part of routine identification and provides further information regarding S. suis virulence and zoonotic potential. Serotypes 2 and 14 possess high zoonotic potential, and serotype 1/2 is the serotype most frequently isolated from diseased pigs in North America. PCR has replaced antibody-based techniques to perform serotyping. However, traditional PCR is not able to differentiate serotype 2 from 1/2 and serotype 1 from 14, given that the only difference in the cps loci of those serotype pairs is a nonsynonymous single-nucleotide polymorphism. We developed a mismatch amplification mutation assay (MAMA)-PCR that was able to correctly serotype 148 isolates previously known to be serotypes 1, 2, 1/2, or 14. This technique will be highly useful in animal and human health laboratories performing PCR serotyping of S. suis isolates.
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Affiliation(s)
- Sonia Lacouture
- Faculty of Veterinary Medicine, University of Montreal, Groupe de Recherche sur les Maladies Infectieuses en Production Animale and Swine and Poultry Infectious Diseases Research Center, Saint-Hyacinthe, Quebec, Canada (Lacouture, Corsaut, Gottschalk).,National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan (Okura, Takamatsu).,The United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan (Takamatsu)
| | - Masatoshi Okura
- Faculty of Veterinary Medicine, University of Montreal, Groupe de Recherche sur les Maladies Infectieuses en Production Animale and Swine and Poultry Infectious Diseases Research Center, Saint-Hyacinthe, Quebec, Canada (Lacouture, Corsaut, Gottschalk).,National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan (Okura, Takamatsu).,The United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan (Takamatsu)
| | - Daisuke Takamatsu
- Faculty of Veterinary Medicine, University of Montreal, Groupe de Recherche sur les Maladies Infectieuses en Production Animale and Swine and Poultry Infectious Diseases Research Center, Saint-Hyacinthe, Quebec, Canada (Lacouture, Corsaut, Gottschalk).,National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan (Okura, Takamatsu).,The United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan (Takamatsu)
| | - Lorelei Corsaut
- Faculty of Veterinary Medicine, University of Montreal, Groupe de Recherche sur les Maladies Infectieuses en Production Animale and Swine and Poultry Infectious Diseases Research Center, Saint-Hyacinthe, Quebec, Canada (Lacouture, Corsaut, Gottschalk).,National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan (Okura, Takamatsu).,The United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan (Takamatsu)
| | - Marcelo Gottschalk
- Faculty of Veterinary Medicine, University of Montreal, Groupe de Recherche sur les Maladies Infectieuses en Production Animale and Swine and Poultry Infectious Diseases Research Center, Saint-Hyacinthe, Quebec, Canada (Lacouture, Corsaut, Gottschalk).,National Institute of Animal Health, National Agriculture and Food Research Organization, Tsukuba, Japan (Okura, Takamatsu).,The United Graduate School of Veterinary Sciences, Gifu University, Gifu, Japan (Takamatsu)
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