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Yamamoto K, Tochikawa S, Miura Y, Matsunobu S, Hirose Y, Eki T. Sensing chemical-induced DNA damage using CRISPR/Cas9-mediated gene-deletion yeast-reporter strains. Appl Microbiol Biotechnol 2024; 108:188. [PMID: 38300351 PMCID: PMC10834598 DOI: 10.1007/s00253-024-13020-w] [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: 07/28/2023] [Revised: 01/09/2024] [Accepted: 01/18/2024] [Indexed: 02/02/2024]
Abstract
Microorganism-based genotoxicity assessments are vital for evaluating potential chemical-induced DNA damage. In this study, we developed both chromosomally integrated and single-copy plasmid-based reporter assays in budding yeast using a RNR3 promoter-driven luciferase gene. These assays were designed to compare the response to genotoxic chemicals with a pre-established multicopy plasmid-based assay. Despite exhibiting the lowest luciferase activity, the chromosomally integrated reporter assay showed the highest fold induction (i.e., the ratio of luciferase activity in the presence and absence of the chemical) compared with the established plasmid-based assay. Using CRISPR/Cas9 technology, we generated mutants with single- or double-gene deletions, affecting major DNA repair pathways or cell permeability. This enabled us to evaluate reporter gene responses to genotoxicants in a single-copy plasmid-based assay. Elevated background activities were observed in several mutants, such as mag1Δ cells, even without exposure to chemicals. However, substantial luciferase induction was detected in single-deletion mutants following exposure to specific chemicals, including mag1Δ, mms2Δ, and rad59Δ cells treated with methyl methanesulfonate; rad59Δ cells exposed to camptothecin; and mms2Δ and rad10Δ cells treated with mitomycin C (MMC) and cisplatin (CDDP). Notably, mms2Δ/rad10Δ cells treated with MMC or CDDP exhibited significantly enhanced luciferase induction compared with the parent single-deletion mutants, suggesting that postreplication and for nucleotide excision repair processes predominantly contribute to repairing DNA crosslinks. Overall, our findings demonstrate the utility of yeast-based reporter assays employing strains with multiple-deletion mutations in DNA repair genes. These assays serve as valuable tools for investigating DNA repair mechanisms and assessing chemical-induced DNA damage. KEY POINTS: • Responses to genotoxic chemicals were investigated in three types of reporter yeast. • Yeast strains with single- and double-deletions of DNA repair genes were tested. • Two DNA repair pathways predominantly contributed to DNA crosslink repair in yeast.
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Affiliation(s)
- Kosuke Yamamoto
- Molecular Genetics Laboratory, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Shintaro Tochikawa
- Molecular Genetics Laboratory, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Yuuki Miura
- Molecular Genetics Laboratory, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Shogo Matsunobu
- Molecular Genetics Laboratory, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Yuu Hirose
- Molecular Genetics Laboratory, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
- Laboratory of Genomics and Photobiology, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan
| | - Toshihiko Eki
- Molecular Genetics Laboratory, Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku-cho, Toyohashi, Aichi, 441-8580, Japan.
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Li J, Ding H, Zhao Y, Lin M, Song L, Wang W, Dong H, Ma X, Liu W, Han L, Zheng F. DNA Repair-Responsive Engineered Whole Cell Microbial Sensors for Sensitive and High-Throughput Screening of Genotoxic Impurities. Anal Chem 2023; 95:12893-12902. [PMID: 37589895 DOI: 10.1021/acs.analchem.3c02245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Genotoxic impurities (GTIs) occurred in drugs, and food and environment pose a threat to human health. Accurate and sensitive evaluation of GTIs is of significance. Ames assay is the existing gold standard method. However, the pathogenic bacteria model lacks metabolic enzymes and requires mass GTIs, leading to insufficient safety, accuracy, and sensitivity. Whole-cell microbial sensors (WCMSs) can use normal strains to simulate the metabolic environment, achieving safe, sensitive, and high-throughput detection and evaluation for GTIs. Here, based on whether GTIs causing DNA alkylation required metabolic enzymes or not, two DNA repair-responsive engineered WCMS systems were constructed including Escherichia coli-WCMS and yeast-WCMS. A DNA repair-responsive promoter as a sensing element was coupled with an enhanced green fluorescent protein as a reporter to construct plasmids for introduction into WCMS. The ada promoter was screened out in the E. coli-WCMS, while the MAG1 promoter was selected for the yeast-WCMS. Different E. coli and yeast strains were modified by gene knockout and mutation to eliminate the interference and enhance the GTI retention in cells and further improved the sensitivity. Finally, GTI consumption of WCMS for the evaluation of methyl methanesulfonate (MMS) and nitrosamines was decreased to 0.46-8.53 μg and 0.068 ng-2.65 μg, respectively, decreasing 2-3 orders of magnitude compared to traditional methods. This study provided a novel approach to measure GTIs with different DNA damage pathways at a molecular level and facilitated the high-throughput screening and sensitive evaluation of GTIs.
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Affiliation(s)
- Jie Li
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
| | - Haotian Ding
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
| | - Yuning Zhao
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
| | - Mingbin Lin
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
| | - Linqi Song
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
| | - Wei Wang
- Chongqing Fuling Institute for Food and Drug Control, Chongqing 408102, China
| | - Haijuan Dong
- The Public Laboratory Platform, China Pharmaceutical University, Nanjing 210009, China
| | - Xiao Ma
- Gansu Institute for Drug Control, Lanzhou 730000, China
| | - Wenyuan Liu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
- Zhejiang Center for Safety Study of Drug Substances (Industrial Technology Innovation Platform), Hangzhou 310018, China
| | - Lingfei Han
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
| | - Feng Zheng
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing 211198, China
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Shu T, Wang J, Li X, Wang X, Wang S. Cytochrome P450 2D6 biosensor for perphenazine based on multi-walled carbon nanotube/ionic liquid and tetrathiafulvalene-tetracyanoquinodimethane salt/ionic liquid gels. Electrochim Acta 2022. [DOI: 10.1016/j.electacta.2022.141656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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Chandra PS, Bajaj A, Desai G, Satyanarayana VA, Sharp HM, Ganjekar S, Supraja TA, Jangam KV, Venkatram L, Kandavel T. Anxiety and depressive symptoms in pregnancy predict low birth weight differentially in male and female infants-findings from an urban pregnancy cohort in India. Soc Psychiatry Psychiatr Epidemiol 2021; 56:2263-2274. [PMID: 34114109 DOI: 10.1007/s00127-021-02106-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 05/10/2021] [Indexed: 11/29/2022]
Abstract
PURPOSE This study examined the contributions of antenatal anxiety, depression, and partner violence to low birth weight (LBW) in infants and to sex-specific birth weight outcomes among mothers from a cohort in urban India. METHODS Data from 700 mothers from the PRAMMS cohort (Prospective Assessment of Maternal Mental Health Study) were used. Pregnant women were assessed in each trimester-T1, T2 and T3, for symptoms of anxiety, and depression as well as partner violence. Multivariate analyses were performed for the whole sample and then for male and female infants separately. The final multivariable logistic regression models were each built using a backward selection procedure and controlling for confounders. To accommodate longitudinally measured data, change in scores (T2-T1 and T3-T2) of anxiety and depression were included in the model. RESULTS Of the 583 women with a singleton live birth, birth weight was available for 514 infants and LBW was recorded in 80 infants (15.6%). Of these, 23 infants were preterm. Overall, higher T1 Depression scores (OR: 1.11; 95% CI 1.040, 1.187) and an increase in both Depression scores (OR: 1.12; 95% CI 1.047, 1.195) from T1 to T2 and Anxiety scores (OR: 1.32; 95% CI 1.079, 1.603) between T2 and T3 were predictors of LBW. Female infants had a higher chance of LBW with increase in maternal anxiety between T1-T2 (OR: 1.69; 95% CI 1.053, 2.708) and T2-T3 (OR: 1.49; 95% CI 1.058, 2.086); partner violence during pregnancy just failed to reach conventional statistical significance (OR: 2.48; 95% CI 0.810, 7.581) in girls. Male infants had a higher chance of LBW with higher baseline depression scores at T1 (OR: 1.23; 95% CI 1.042, 1.452) and an increase in depression scores (OR: 1.25; 95% CI 1.060, 1.472) from T1 to T2. CONCLUSION Increasing prenatal anxiety and depressive symptoms in different trimesters of pregnancy were associated with LBW with sex-specific patterns of association in this sample from a Low and Middle Income Country.
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Affiliation(s)
- Prabha S Chandra
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bangalore, India.
| | - Aakash Bajaj
- Department of Biostatistics, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Geetha Desai
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Veena A Satyanarayana
- Department of Clinical Psychology, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Helen M Sharp
- Department of Psychological Science, University of Liverpool, Liverpool, UK
| | - Sundarnag Ganjekar
- Department of Psychiatry, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - T A Supraja
- Department of Psychiatric Social Work, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Kavita V Jangam
- Department of Psychiatric Social Work, National Institute of Mental Health and Neurosciences, Bangalore, India
| | - Latha Venkatram
- Department of Obstetrics, Rangadore Memorial Hospital, Bangalore, India
| | - Thennarasu Kandavel
- Department of Biostatistics, National Institute of Mental Health and Neurosciences, Bangalore, India
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Jiang L, Huang L, Cai J, Xu Z, Lian J. Functional expression of eukaryotic cytochrome P450s in yeast. Biotechnol Bioeng 2020; 118:1050-1065. [PMID: 33205834 DOI: 10.1002/bit.27630] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 09/28/2020] [Accepted: 11/11/2020] [Indexed: 12/22/2022]
Abstract
Cytochrome P450 enzymes (P450s) are a superfamily of heme-thiolate proteins widely existing in various organisms. Due to their key roles in secondary metabolism, degradation of xenobiotics, and carcinogenesis, there is a great demand to heterologously express and obtain a sufficient amount of active eukaryotic P450s. However, most eukaryotic P450s are endoplasmic reticulum-localized membrane proteins, which is the biggest challenge for functional expression to high levels. Furthermore, the functions of P450s require the cooperation of cytochrome P450 reductases for electron transfer. Great efforts have been devoted to the heterologous expression of eukaryotic P450s, and yeasts, particularly Saccharomyces cerevisiae are frequently considered as the first expression systems to be tested for this challenging purpose. This review discusses the strategies for improving the expression and activity of eukaryotic P450s in yeasts, followed by examples of P450s involved in biosynthetic pathway engineering.
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Affiliation(s)
- Lihong Jiang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- Center for Synthetic Biology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Lei Huang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Jin Cai
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
- Center for Synthetic Biology, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, China
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Martin-Yken H. Yeast-Based Biosensors: Current Applications and New Developments. BIOSENSORS 2020; 10:E51. [PMID: 32413968 PMCID: PMC7277604 DOI: 10.3390/bios10050051] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/17/2020] [Accepted: 04/20/2020] [Indexed: 12/23/2022]
Abstract
Biosensors are regarded as a powerful tool to detect and monitor environmental contaminants, toxins, and, more generally, organic or chemical markers of potential threats to human health. They are basically composed of a sensor part made up of either live cells or biological active molecules coupled to a transducer/reporter technological element. Whole-cells biosensors may be based on animal tissues, bacteria, or eukaryotic microorganisms such as yeasts and microalgae. Although very resistant to adverse environmental conditions, yeasts can sense and respond to a wide variety of stimuli. As eukaryotes, they also constitute excellent cellular models to detect chemicals and organic contaminants that are harmful to animals. For these reasons, combined with their ease of culture and genetic modification, yeasts have been commonly used as biological elements of biosensors since the 1970s. This review aims first at giving a survey on the different types of yeast-based biosensors developed for the environmental and medical domains. We then present the technological developments currently undertaken by academic and corporate scientists to further drive yeasts biosensors into a new era where the biological element is optimized in a tailor-made fashion by in silico design and where the output signals can be recorded or followed on a smartphone.
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Affiliation(s)
- Helene Martin-Yken
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), UMR 792 Toulouse Biotechnology Institute (TBI), 31400 Toulouse, France; ; Tel.: +689-89-52-31-88
- Institut de Recherche pour le Développement (IRD), Faa’a, 98702 Tahiti, French Polynesia
- Unite Mixte de Recherche n°241 Ecosystemes Insulaires et Oceaniens, Université de la Polynésie Française, Faa’a, 98702 Tahiti, French Polynesia
- Laboratoire de Recherche sur les Biotoxines Marines, Institut Louis Malardé, Papeete, 98713 Tahiti, French Polynesia
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NDMA impurity in valsartan and other pharmaceutical products: Analytical methods for the determination of N-nitrosamines. J Pharm Biomed Anal 2019; 164:536-549. [DOI: 10.1016/j.jpba.2018.11.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/27/2018] [Accepted: 11/04/2018] [Indexed: 12/18/2022]
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Overview of Piezoelectric Biosensors, Immunosensors and DNA Sensors and Their Applications. MATERIALS 2018; 11:ma11030448. [PMID: 29562700 PMCID: PMC5873027 DOI: 10.3390/ma11030448] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Revised: 03/16/2018] [Accepted: 03/18/2018] [Indexed: 12/20/2022]
Abstract
Piezoelectric biosensors are a group of analytical devices working on a principle of affinity interaction recording. A piezoelectric platform or piezoelectric crystal is a sensor part working on the principle of oscillations change due to a mass bound on the piezoelectric crystal surface. In this review, biosensors having their surface modified with an antibody or antigen, with a molecularly imprinted polymer, with genetic information like single stranded DNA, and biosensors with bound receptors of organic of biochemical origin, are presented and discussed. The mentioned recognition parts are frequently combined with use of nanoparticles and applications in this way are also introduced. An overview of the current literature is given and the methods presented are commented upon.
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Yeast-based genotoxicity tests for assessing DNA alterations and DNA stress responses: a 40-year overview. Appl Microbiol Biotechnol 2018; 102:2493-2507. [PMID: 29423630 DOI: 10.1007/s00253-018-8783-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 01/12/2018] [Accepted: 01/14/2018] [Indexed: 10/18/2022]
Abstract
By damaging DNA molecules, genotoxicants cause genetic mutations and also increase human susceptibility to cancers and genetic diseases. Over the past four decades, several assays have been developed in the budding yeast Saccharomyces cerevisiae to screen potential genotoxic substances and provide alternatives to animal-based genotoxicity tests. These yeast-based genotoxicity tests are either DNA alteration-based or DNA stress-response reporter-based. The former, which came first, were developed from the genetic studies conducted on various types of DNA alterations in yeast cells. Despite their limited throughput capabilities, some of these tests have been used as short-term genotoxicity tests in addition to bacteria- or mammalian cell-based tests. In contrast, the latter tests are based on the emergent transcriptional induction of DNA repair-related genes via activation of the DNA damage checkpoint kinase cascade triggered by DNA damage. Some of these reporter assays have been linked to DNA damage-responsive promoters to assess chemical carcinogenicity and ecotoxicity in environmental samples. Yeast-mediated genotoxicity tests are being continuously improved by increasing the permeability of yeast cell walls, by the ectopic expression of mammalian cytochrome P450 systems, by the use of DNA repair-deficient host strains, and by integrating them into high-throughput formats or microfluidic devices. Notably, yeast-based reporter assays linked with the newer toxicogenomic approaches are becoming powerful short-term genotoxicity tests for large numbers of compounds. These tests can also be used to detect polluted environmental samples, and as effective screening tools during anticancer drug development.
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