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Tanvir R, Ijaz S, Sajid I, Hasnain S. Multifunctional in vitro, in silico and DFT analyses on antimicrobial BagremycinA biosynthesized by Micromonospora chokoriensis CR3 from Hieracium canadense. Sci Rep 2024; 14:10976. [PMID: 38745055 PMCID: PMC11093986 DOI: 10.1038/s41598-024-61490-9] [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: 11/19/2023] [Accepted: 05/06/2024] [Indexed: 05/16/2024] Open
Abstract
Among the actinomycetes in the rare genera, Micromonospora is of great interest since it has been shown to produce novel therapeutic compounds. Particular emphasis is now on its isolation from plants since its population from soil has been extensively explored. The strain CR3 was isolated as an endophyte from the roots of Hieracium canadense, and it was identified as Micromonospora chokoriensis through 16S gene sequencing and phylogenetic analysis. The in-vitro analysis of its extract revealed it to be active against the clinical isolates of methicillin-resistant Staphylococcus aureus (MRSA) and Candida tropicalis (15 mm). No bioactivity was observed against Gram-negative bacteria, Escherichia coli ATCC 25922, and Klebsiella pneumoniae ATCC 706003. The Micromonospora chokoriensis CR3 extract was also analyzed through the HPLC-DAD-UV-VIS resident database, and it gave a maximum match factor of 997.334 with the specialized metabolite BagremycinA (BagA). The in-silico analysis indicated that BagA strongly interacted with the active site residues of the sterol 14-α demethylase and thymidylate kinase enzymes, with the lowest binding energies of - 9.7 and - 8.3 kcal/mol, respectively. Furthermore, the normal mode analysis indicated that the interaction between these proteins and BagA was stable. The DFT quantum chemical properties depicted BagA to be reasonably reactive with a HOMO-LUMO gap of (ΔE) of 4.390 eV. BagA also passed the drug-likeness test with a synthetic accessibility score of 2.06, whereas Protox-II classified it as a class V toxicity compound with high LD50 of 2644 mg/kg. The current study reports an endophytic actinomycete, M. chokoriensis, associated with H. canadense producing the bioactive metabolite BagA with promising antimicrobial activity, which can be further modified and developed into a safe antimicrobial drug.
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Affiliation(s)
- Rabia Tanvir
- Institute of Microbiology (IOM), University of Veterinary and Animal Sciences (UVAS), Lahore, 54000, Punjab, Pakistan.
| | - Saadia Ijaz
- Department of Microbiology and Molecular Genetics, The Women University, Multan, 66000, Punjab, Pakistan
| | - Imran Sajid
- Institute of Microbiology and Molecular Genetics (IMMG), University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Punjab, Pakistan
| | - Shahida Hasnain
- Institute of Microbiology and Molecular Genetics (IMMG), University of the Punjab, Quaid-e-Azam Campus, Lahore, 54590, Punjab, Pakistan
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Riera-Ruiz C, Moriyama H. Enzyme kinetics of deoxyuridine triphosphatase from Western corn rootworm. BMC Res Notes 2023; 16:336. [PMID: 37974243 PMCID: PMC10652518 DOI: 10.1186/s13104-023-06618-2] [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: 07/31/2023] [Accepted: 11/07/2023] [Indexed: 11/19/2023] Open
Abstract
OBJECTIVE The Western corn rootworm (WCR), Diabrotica virgifera virgifera, is a highly adaptable insect pest that has evolved resistance to a variety of control strategies, including insecticides. Therefore, it is interesting to examine how housekeeping proteins in WCR have been changed under WCR-controlling strategies. In this study, we focused on one of such proteins in WCR, a ubiquitous enzyme 5'-triphosphate nucleotidohydrolase (dUTPase). In the thymidine synthetic pathway, dUTPase hydrolyzes deoxyuridine triphosphate (dUTP) and supplies the substrate, deoxyuridine monophosphate, for the thymidylate synthase (TS). It decreases the cellular content of uracil, reducing uracil misincorporation into DNA. Suppressing the dUTPase activity, therefore, contributes to thymineless death. In this study, we investigated the enzymatic properties of dUTPase. RESULTS The WCR dUTPase gene (DUT) was synthesized with the addition of His-tag corresponding DNA sequence and then cloned and expressed in Escherichia coli, and the protein product was purified. The product of WCR DUT hydrolyzed dUTP and was designated as dUTPase. WCR dUTPase did not hydrolyze dATP, dTTP, dCTP, or dGTP. WCR dUTPase was analyzed via size-exclusion chromatography and exhibited a molecular weight corresponding to that of trimer. The present format can be interpreted as nuclear trimer type. Possible isomers will be examined once transcriptome analyses are conducted.
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Affiliation(s)
- Carlos Riera-Ruiz
- School of Biological Sciences, University of Nebraska-Lincoln, 243 Manter Hall, Lincoln, NE, 68588-0118, USA
- Escuela Superior Politécnica del Litoral, Centro de Investigaciones Biotecnológicas del Ecuador, ESPOL Polytechnic University, ESPOL, Campus Gustavo Galindo Km 30.5 Vía Perimetral, P.O Box 09-01-5863, Guayaquil, Ecuador
| | - Hideaki Moriyama
- School of Biological Sciences, University of Nebraska-Lincoln, 243 Manter Hall, Lincoln, NE, 68588-0118, USA.
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Krishnan K, Katneni VK, Prabhudas SK, Kaikkolante N, Jangam AK, Katneni UK, Hauton C, Peruzza L, Mudagandur SS, Koyadan VK, Poochirian JK, Jena J. MRF: a tool to overcome the barrier of inconsistent genome annotations and perform comparative genomics studies for the largest animal DNA virus. Virol J 2023; 20:72. [PMID: 37072853 PMCID: PMC10111743 DOI: 10.1186/s12985-023-02035-w] [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: 11/29/2022] [Accepted: 04/09/2023] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND The genome of the largest known animal virus, the white spot syndrome virus (WSSV) responsible for huge economic losses and loss of employment in aquaculture, suffers from inconsistent annotation nomenclature. Novel genome sequence, circular genome and variable genome length led to nomenclature inconsistencies. Since vast knowledge has already accumulated in the past two decades with inconsistent nomenclature, the insights gained on a genome could not be easily extendable to other genomes. Therefore, the present study aims to perform comparative genomics studies in WSSV on uniform nomenclature. METHODS We have combined the standard mummer tool with custom scripts to develop missing regions finder (MRF) that documents the missing genome regions and coding sequences in virus genomes in comparison to a reference genome and in its annotation nomenclature. The procedure was implemented as web tool and in command-line interface. Using MRF, we have documented the missing coding sequences in WSSV and explored their role in virulence through application of phylogenomics, machine learning models and homologous genes. RESULTS We have tabulated and depicted the missing genome regions, missing coding sequences and deletion hotspots in WSSV on a common annotation nomenclature and attempted to link them to virus virulence. It was observed that the ubiquitination, transcription regulation and nucleotide metabolism might be essentially required for WSSV pathogenesis; and the structural proteins, VP19, VP26 and VP28 are essential for virus assembly. Few minor structural proteins in WSSV would act as envelope glycoproteins. We have also demonstrated the advantage of MRF in providing detailed graphic/tabular output in less time and also in handling of low-complexity, repeat-rich and highly similar regions of the genomes using other virus cases. CONCLUSIONS Pathogenic virus research benefits from tools that could directly indicate the missing genomic regions and coding sequences between isolates/strains. In virus research, the analyses performed in this study provides an advancement to find the differences between genomes and to quickly identify the important coding sequences/genomes that require early attention from researchers. To conclude, the approach implemented in MRF complements similarity-based tools in comparative genomics involving large, highly-similar, length-varying and/or inconsistently annotated viral genomes.
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Affiliation(s)
- Karthic Krishnan
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
| | - Vinaya Kumar Katneni
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India.
| | - Sudheesh K Prabhudas
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
| | - Nimisha Kaikkolante
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
| | - Ashok Kumar Jangam
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
| | - Upendra Kumar Katneni
- The Center for Blood Oxygen Transport and Hemostasis, Department of Pediatrics, University of Maryland School of Medicine, Maryland, USA
| | - Chris Hauton
- Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton Waterfront Campus, Southampton, UK
| | - Luca Peruzza
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padua, Italy
| | - Shashi Shekhar Mudagandur
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
| | - Vijayan K Koyadan
- Centre for Bioinformatics, Nutrition Genetics and Biotechnology Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
| | - Jithendran Karingalakkandy Poochirian
- Aquatic Animal Health and Environment Division, ICAR - Central Institute of Brackishwater Aquaculture, 75, Santhome High Road, MRC Nagar, RA Puram, Chennai, Tamil Nadu, 600028, India
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LaCourse KD, Zepeda-Rivera M, Kempchinsky AG, Baryiames A, Minot SS, Johnston CD, Bullman S. The cancer chemotherapeutic 5-fluorouracil is a potent Fusobacterium nucleatum inhibitor and its activity is modified by intratumoral microbiota. Cell Rep 2022; 41:111625. [PMID: 36384132 PMCID: PMC10790632 DOI: 10.1016/j.celrep.2022.111625] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 08/26/2022] [Accepted: 10/17/2022] [Indexed: 11/17/2022] Open
Abstract
Fusobacterium nucleatum (Fn) is a dominant bacterial species in colorectal cancer (CRC) tissue that is associated with cancer progression and poorer patient prognosis. Following a small-molecule inhibitor screen of 1,846 bioactive compounds against a Fn CRC isolate, we find that 15% of inhibitors are antineoplastic agents including fluoropyrimidines. Validation of these findings reveals that 5-fluorouracil (5-FU), a first-line CRC chemotherapeutic, is a potent inhibitor of Fn CRC isolates. We also identify members of the intratumoral microbiota, including Escherichia coli, that are resistant to 5-FU. Further, CRC E. coli isolates can modify 5-FU and relieve 5-FU toxicity toward otherwise-sensitive Fn and human CRC epithelial cells. Lastly, we demonstrate that ex vivo patient CRC tumor microbiota undergo community disruption after 5-FU exposure and have the potential to deplete 5-FU levels, reducing local drug efficacy. Together, these observations argue for further investigation into the role of the CRC intratumoral microbiota in patient response to chemotherapy.
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Affiliation(s)
- Kaitlyn D LaCourse
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Martha Zepeda-Rivera
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Andrew G Kempchinsky
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Alexander Baryiames
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA
| | - Samuel S Minot
- Data Core, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Christopher D Johnston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA.
| | - Susan Bullman
- Human Biology Division, Fred Hutchinson Cancer Center, 1100 Fairview Ave N, Seattle, WA 98109, USA.
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5
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Spanogiannopoulos P, Kyaw TS, Guthrie BGH, Bradley PH, Lee JV, Melamed J, Malig YNA, Lam KN, Gempis D, Sandy M, Kidder W, Van Blarigan EL, Atreya CE, Venook A, Gerona RR, Goga A, Pollard KS, Turnbaugh PJ. Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism. Nat Microbiol 2022; 7:1605-1620. [PMID: 36138165 PMCID: PMC9530025 DOI: 10.1038/s41564-022-01226-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 08/03/2022] [Indexed: 12/15/2022]
Abstract
Pharmaceuticals have extensive reciprocal interactions with the microbiome, but whether bacterial drug sensitivity and metabolism is driven by pathways conserved in host cells remains unclear. Here we show that anti-cancer fluoropyrimidine drugs inhibit the growth of gut bacterial strains from 6 phyla. In both Escherichia coli and mammalian cells, fluoropyrimidines disrupt pyrimidine metabolism. Proteobacteria and Firmicutes metabolized 5-fluorouracil to its inactive metabolite dihydrofluorouracil, mimicking the major host mechanism for drug clearance. The preTA operon was necessary and sufficient for 5-fluorouracil inactivation by E. coli, exhibited high catalytic efficiency for the reductive reaction, decreased the bioavailability and efficacy of oral fluoropyrimidine treatment in mice and was prevalent in the gut microbiomes of colorectal cancer patients. The conservation of both the targets and enzymes for metabolism of therapeutics across domains highlights the need to distinguish the relative contributions of human and microbial cells to drug efficacy and side-effect profiles.
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Affiliation(s)
- Peter Spanogiannopoulos
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Than S Kyaw
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Ben G H Guthrie
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Patrick H Bradley
- Gladstone Institutes, San Francisco, CA, USA
- Department of Microbiology, The Ohio State University, Columbus, OH, USA
| | - Joyce V Lee
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Jonathan Melamed
- Clinical Toxicology and Environmental Biomonitoring Laboratory, University of California San Francisco, San Francisco, CA, USA
| | - Ysabella Noelle Amora Malig
- Clinical Toxicology and Environmental Biomonitoring Laboratory, University of California San Francisco, San Francisco, CA, USA
| | - Kathy N Lam
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Daryll Gempis
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Moriah Sandy
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Wesley Kidder
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Erin L Van Blarigan
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
| | - Chloe E Atreya
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Alan Venook
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Roy R Gerona
- Clinical Toxicology and Environmental Biomonitoring Laboratory, University of California San Francisco, San Francisco, CA, USA
| | - Andrei Goga
- Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA, USA
- UCSF Helen Diller Family Comprehensive Cancer Center, San Francisco, CA, USA
| | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Peter J Turnbaugh
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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6
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Spizzichino S, Boi D, Boumis G, Lucchi R, Liberati FR, Capelli D, Montanari R, Pochetti G, Piacentini R, Parisi G, Paone A, Rinaldo S, Contestabile R, Tramonti A, Paiardini A, Giardina G, Cutruzzolà F. Cytosolic localization and in vitro assembly of human de novo thymidylate synthesis complex. FEBS J 2021; 289:1625-1649. [PMID: 34694685 PMCID: PMC9299187 DOI: 10.1111/febs.16248] [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: 08/21/2021] [Accepted: 10/21/2021] [Indexed: 11/27/2022]
Abstract
De novo thymidylate synthesis is a crucial pathway for normal and cancer cells. Deoxythymidine monophosphate (dTMP) is synthesized by the combined action of three enzymes: serine hydroxymethyltransferase (SHMT1), dihydrofolate reductase (DHFR) and thymidylate synthase (TYMS), with the latter two being targets of widely used chemotherapeutics such as antifolates and 5‐fluorouracil. These proteins translocate to the nucleus after SUMOylation and are suggested to assemble in this compartment into the thymidylate synthesis complex. We report the intracellular dynamics of the complex in cancer cells by an in situ proximity ligation assay, showing that it is also detected in the cytoplasm. This result indicates that the role of the thymidylate synthesis complex assembly may go beyond dTMP synthesis. We have successfully assembled the dTMP synthesis complex in vitro, employing tetrameric SHMT1 and a bifunctional chimeric enzyme comprising human thymidylate synthase and dihydrofolate reductase. We show that the SHMT1 tetrameric state is required for efficient complex assembly, indicating that this aggregation state is evolutionarily selected in eukaryotes to optimize protein–protein interactions. Lastly, our results regarding the activity of the complete thymidylate cycle in vitro may provide a useful tool with respect to developing drugs targeting the entire complex instead of the individual components.
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Affiliation(s)
- Sharon Spizzichino
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Dalila Boi
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Giovanna Boumis
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Roberta Lucchi
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | | | - Davide Capelli
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Roberta Montanari
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Giorgio Pochetti
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Roberta Piacentini
- Center for Life Nano & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Giacomo Parisi
- Center for Life Nano & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), Rome, Italy
| | - Alessio Paone
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Serena Rinaldo
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | | | - Angela Tramonti
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy.,Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy
| | | | - Giorgio Giardina
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy
| | - Francesca Cutruzzolà
- Department of Biochemical Sciences, Sapienza University of Rome, Rome, Italy.,Laboratory affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Rome, Italy
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7
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Chen JY, Chen HJ, Chen PF. Association of expression and genotypes of thymidylate synthase in non-small cell lung cancer patients with different clinicopathological characteristics. Pteridines 2021. [DOI: 10.1515/pteridines-2020-0013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Abstract
Objective
To explore the expression and genotypes of thymidylate synthase (TS) in patients of non-small cell lung cancer (NSCLC) with different clinicopathological characteristics.
Methods
The expression profiles of TS were examined by immunohistochemical staining and quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) in 160 patients with NSCLC. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used to detect TS-5′UTR tandem repeats, G/C nucleotide polymorphisms, and 3′UTR 6 bp deletion/insertion polymorphisms. The relationships between clinicopathological characteristics and TS expression or genotypes were investigated through χ
2 test. Kaplan–Meier survival analysis was used to analyze the association between TS expression and overall survival (OS) and disease-free survival (DFS) of NSCLC patients.
Results
The expression levels of TS protein and TS gene in NSCLC tissues were significantly higher than that in paracancerous tissues (P < 0.05). Furthermore, high expression of TS protein and 5′UTR polymorphism of TS gene showed significant correlation with differentiation, TNM stage, and lymph node metastases. The frequency of −6 bp/−6 bp genotypes in patients with NSCLC was 43.13% (69/160), which was higher than others. In addition, the rate of TS protein overexpression in NSCLC patients with 3R/3R was 79.79%, which was higher than others. Interestingly, high expression of TS protein predicted shorter DFS and OS and lower 3-year DFS rate and 3-year OS rate.
Conclusions
The expression levels of TS in NSCLC were significantly increased and may help to predict the prognosis of NSCLC, and high expression of TS protein and 5′UTR polymorphism of TS gene were significantly related to differentiation, TNM stage, and lymph node metastases.
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Affiliation(s)
- Jin-Yin Chen
- Department of Respiratory Medicine, Zhuji Affiliated Hospital of Wenzhou Medical University (Zhuji People’s Hospital of Zhejiang Province), 9 Jianmin Street, Taozhu Sub-district, Zhuji , Zhejiang 311800 , China
| | - He-Jian Chen
- Department of Respiratory Medicine, Zhuji Affiliated Hospital of Wenzhou Medical University (Zhuji People’s Hospital of Zhejiang Province), 9 Jianmin Street, Taozhu Sub-district, Zhuji , Zhejiang 311800 , China
| | - Pei-Feng Chen
- Department of Respiratory Medicine, Zhuji Affiliated Hospital of Wenzhou Medical University (Zhuji People’s Hospital of Zhejiang Province), 9 Jianmin Street, Taozhu Sub-district, Zhuji , Zhejiang 311800 , China
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Detection of Genomic Uracil Patterns. Int J Mol Sci 2021; 22:ijms22083902. [PMID: 33918885 PMCID: PMC8070346 DOI: 10.3390/ijms22083902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/28/2021] [Accepted: 04/05/2021] [Indexed: 01/06/2023] Open
Abstract
The appearance of uracil in the deoxyuridine moiety of DNA is among the most frequently occurring genomic modifications. Three different routes can result in genomic uracil, two of which do not require specific enzymes: spontaneous cytosine deamination due to the inherent chemical reactivity of living cells, and thymine-replacing incorporation upon nucleotide pool imbalances. There is also an enzymatic pathway of cytosine deamination with multiple DNA (cytosine) deaminases involved in this process. In order to describe potential roles of genomic uracil, it is of key importance to utilize efficient uracil-DNA detection methods. In this review, we provide a comprehensive and critical assessment of currently available uracil detection methods with special focus on genome-wide mapping solutions. Recent developments in PCR-based and in situ detection as well as the quantitation of genomic uracil are also discussed.
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Pathania S, Khan MI, Kumar A, Gupta AK, Rani K, Ramesh Parashar T, Jayaram J, Ranjan Mishra P, Srivastava A, Mathur S, Hari S, Hariprasad G. Proteomics of Sentinel Lymph Nodes in Early Breast Cancer for Identification of Thymidylate Synthase as a Potential Biomarker to Flag Metastasis: A Preliminary Study. Cancer Manag Res 2020; 12:4841-4854. [PMID: 32606973 PMCID: PMC7320752 DOI: 10.2147/cmar.s255684] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/21/2020] [Indexed: 12/30/2022] Open
Abstract
Introduction Breast cancer is the second most common cancer in women across the world. Some of the patients who present in the early stage of disease are affected by metastasis to the axillary group of lymph nodes. The first among this group that is affected is called as sentinel lymph node, and its diagnosis is crucial for the staging of cancer thereby dictating the type of surgical therapy. Therefore, the sentinel lymph node status provides the most relevant information to the surgeon and patient prognosis. The expanded utilization of breast conservation surgery has declined the morbidity associated with mastectomy and axillary lymph node surgery. Recent interest is, therefore, centered on techniques that allow accurate assessment of the sentinel lymph node metastasis. A current procedure such as sentinel lymph node biopsy (SLNB) that is used to assess axillary lymph node metastasis is neither specific nor sensitive, and besides, it is time-consuming. Objective To compare the protein profiles between metastatic and non-metastatic lymph nodes to identify a biomarker that can flag lymph node metastasis. Materials and Methods Women with early breast cancer were screened using mammography imaging and recruited to the study. Surgical resection was done to remove the breast tissue, and sentinel lymph node was identified using fluorescein and methylene blue tracer. Lymph node was sliced, and one set was sent for histopathology, which was considered the gold standard to assess the metastatic status of the lymph node. One set of slices was taken for proteomic experiments. Proteins were labelled with fluorescent cyanine tags and were subjected to difference gel electrophoresis experiment. Differentially expressed spots that had at least a twofold relative ratio and consistent pattern across three sets of biological replicate experiments were marked. Gel spots were trypsin digested and identified on mass spectrometry machine. Validation study was done by Western blot experiment on the same set of samples. Results Thymidylate synthase has a twofold higher expression in the metastatic sentinel lymph nodes as compared to non-metastatic lymph nodes in early breast cancer patients. Conclusion Differential in gel expression proteomics is an ideal platform for the identification of potential protein biomarker candidates that can differentiate metastatic from non-metastatic lymph nodes in early breast cancer. The identification of thymidylate synthase offers a scope to develop an on-table diagnostic kit to assess the status of sentinel lymph nodes during mastectomy procedure to guide surgical management of axillary lymph nodes in early breast cancer. ![]()
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Affiliation(s)
- Sheetal Pathania
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Mohd Imran Khan
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Abhishek Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Ashish Kumar Gupta
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Komal Rani
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Tanvi Ramesh Parashar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Jnaneshwari Jayaram
- Department of Surgery, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Piyush Ranjan Mishra
- Department of Surgery, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Anurag Srivastava
- Department of Surgery, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Sandeep Mathur
- Department of Pathology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Smriti Hari
- Department of Radiology, All India Institute of Medical Sciences, New Delhi 110029, India
| | - Gururao Hariprasad
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
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Pozzi C, Lopresti L, Tassone G, Mangani S. Targeting Methyltransferases in Human Pathogenic Bacteria: Insights into Thymidylate Synthase (TS) and Flavin-Dependent TS (FDTS). Molecules 2019; 24:molecules24081638. [PMID: 31027295 PMCID: PMC6514825 DOI: 10.3390/molecules24081638] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 04/18/2019] [Accepted: 04/25/2019] [Indexed: 01/10/2023] Open
Abstract
In cells, thymidylate synthases provide the only de novo source of 2′-deoxythymidine-5′-monophosphate (dTMP), required for DNA synthesis. The activity of these enzymes is pivotal for cell survival and proliferation. Two main families of thymidylate synthases have been identified in bacteria, folate-dependent thymidylate synthase (TS) and flavin-dependent TS (FDTS). TS and FDTS are highly divergent enzymes, characterized by exclusive catalytic mechanisms, involving different sets of cofactors. TS and FDTS mechanisms of action have been recently revised, providing new perspectives for the development of antibacterial drugs targeting these enzymes. Nonetheless, some catalytic details still remain elusive. For bacterial TSs, half-site reactivity is still an open debate and the recent evidences are somehow controversial. Furthermore, different behaviors have been identified among bacterial TSs, compromising the definition of common mechanisms. Moreover, the redox reaction responsible for the regeneration of reduced flavin in FDTSs is not completely clarified. This review describes the recent advances in the structural and functional characterization of bacterial TSs and FDTSs and the current understanding of their mechanisms of action. Furthermore, the recent progresses in the development of inhibitors targeting TS and FDTS in human pathogenic bacteria are summarized.
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Affiliation(s)
- Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy⁻Department of Excellence 2018-2020, University of Siena, via Aldo Moro 2, 53100 Siena, Italy.
| | - Ludovica Lopresti
- Department of Biotechnology, Chemistry and Pharmacy⁻Department of Excellence 2018-2020, University of Siena, via Aldo Moro 2, 53100 Siena, Italy.
| | - Giusy Tassone
- Department of Biotechnology, Chemistry and Pharmacy⁻Department of Excellence 2018-2020, University of Siena, via Aldo Moro 2, 53100 Siena, Italy.
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy⁻Department of Excellence 2018-2020, University of Siena, via Aldo Moro 2, 53100 Siena, Italy.
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