1
|
He J, Li J, Luo M, Liu Y, Sun J, Yao L. Identification of two novel linear epitopes on the E165R protein of African swine fever virus recognized by monoclonal antibodies. Front Vet Sci 2024; 11:1392350. [PMID: 39166172 PMCID: PMC11333337 DOI: 10.3389/fvets.2024.1392350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 07/24/2024] [Indexed: 08/22/2024] Open
Abstract
African swine fever (ASF) is a highly fatal infectious disease in pigs, caused by the African swine fever virus (ASFV). It is characterized by short disease duration and high morbidity and mortality. In August 2018, ASF was first reported in China and it subsequently spread rapidly throughout the country, causing serious economic losses for the Chinese pig industry. Early detection plays a critical role in preventing and controlling ASF because there is currently no effective vaccine or targeted therapeutic medication available. Additionally, identifying conserved protective antigenic epitopes of ASFV is essential for the development of diagnostic reagents. The E165R protein, which is highly expressed in the early stages of ASFV infection, can serve as an important indicator for early detection. In this study, we successfully obtained high purity soluble prokaryotic expression of the E165R protein. We then utilized the purified recombinant E165R protein for immunization in mice to prepare monoclonal antibodies (mAbs) using the hybridoma fusion technique. After three subclonal screens, we successfully obtained three mAbs against ASFV E165R protein in cells named 1B7, 1B8, and 10B8. Through immunofluorescence assay (IFA) and Western blot, we confirmed that the prepared mAbs specifically recognize the baculovirus-expressed E165R protein. By using overlapping truncated E165R protein and overlapping peptide scanning analysis, we tentatively identified two novel linear B cell epitopes (13EAEAYYPPSV22 and 55VACEHMGKKC64) that are highly conserved in genotype I and genotype II of ASFV. Thus, as a detection antibody, it has the capability to detect ASFV across a wide range of genotypes, providing valuable information for the development of related immunodiagnostic reagents.
Collapse
Affiliation(s)
- Jian He
- Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Field Observation and Research Station of Headwork Wetland Ecosystem of The Central Route of South-to-North Water Diversion Project, School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Jieqiong Li
- Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Field Observation and Research Station of Headwork Wetland Ecosystem of The Central Route of South-to-North Water Diversion Project, School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Mingzhan Luo
- Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Field Observation and Research Station of Headwork Wetland Ecosystem of The Central Route of South-to-North Water Diversion Project, School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Yangkun Liu
- Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Field Observation and Research Station of Headwork Wetland Ecosystem of The Central Route of South-to-North Water Diversion Project, School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| | - Jingchen Sun
- Guangdong Provincial Key Laboratory of Agro-animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Lunguang Yao
- Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Field Observation and Research Station of Headwork Wetland Ecosystem of The Central Route of South-to-North Water Diversion Project, School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang, China
| |
Collapse
|
2
|
Saha D, Pramanik A, Freville A, Siddiqui AA, Pal U, Banerjee C, Nag S, Debsharma S, Pramanik S, Mazumder S, Maiti NC, Datta S, van Ooij C, Bandyopadhyay U. Structure-function analysis of nucleotide housekeeping protein HAM1 from human malaria parasite Plasmodium falciparum. FEBS J 2024. [PMID: 39003571 DOI: 10.1111/febs.17216] [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: 01/20/2024] [Revised: 03/29/2024] [Accepted: 06/20/2024] [Indexed: 07/15/2024]
Abstract
Non-canonical nucleotides, generated as oxidative metabolic by-products, significantly threaten the genome integrity of Plasmodium falciparum and thereby, their survival, owing to their mutagenic effects. PfHAM1, an evolutionarily conserved inosine/xanthosine triphosphate pyrophosphohydrolase, maintains nucleotide homeostasis in the malaria parasite by removing non-canonical nucleotides, although structure-function intricacies are hitherto poorly reported. Here, we report the X-ray crystal structure of PfHAM1, which revealed a homodimeric structure, additionally validated by size-exclusion chromatography-multi-angle light scattering analysis. The two monomeric units in the dimer were aligned in a parallel fashion, and critical residues associated with substrate and metal binding were identified, wherein a notable structural difference was observed in the β-sheet main frame compared to human inosine triphosphate pyrophosphatase. PfHAM1 exhibited Mg++-dependent pyrophosphohydrolase activity and the highest binding affinity to dITP compared to other non-canonical nucleotides as measured by isothermal titration calorimetry. Modifying the pfham1 genomic locus followed by live-cell imaging of expressed mNeonGreen-tagged PfHAM1 demonstrated its ubiquitous presence in the cytoplasm across erythrocytic stages with greater expression in trophozoites and schizonts. Interestingly, CRISPR-Cas9/DiCre recombinase-guided pfham1-null P. falciparum survived in culture under standard growth conditions, indicating its assistive role in non-canonical nucleotide clearance during intra-erythrocytic stages. This is the first comprehensive structural and functional report of PfHAM1, an atypical nucleotide-cleansing enzyme in P. falciparum.
Collapse
Affiliation(s)
- Debanjan Saha
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Atanu Pramanik
- Division of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Aline Freville
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, UK
| | - Asim Azhar Siddiqui
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Uttam Pal
- Division of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Chinmoy Banerjee
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Shiladitya Nag
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Subhashis Debsharma
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Saikat Pramanik
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Somnath Mazumder
- Department of Zoology, Raja Peary Mohan College, Uttarpara, India
| | - Nakul C Maiti
- Division of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Saumen Datta
- Division of Structural Biology & Bioinformatics, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Christiaan van Ooij
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, UK
| | - Uday Bandyopadhyay
- Division of Infectious Diseases and Immunology, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Department of Biological Sciences, Bose Institute, Kolkata, India
| |
Collapse
|
3
|
Rácz GA, Nagy N, Várady G, Tóvári J, Apáti Á, Vértessy BG. Discovery of two new isoforms of the human DUT gene. Sci Rep 2023; 13:7760. [PMID: 37173337 PMCID: PMC10181998 DOI: 10.1038/s41598-023-32970-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 04/05/2023] [Indexed: 05/15/2023] Open
Abstract
In human cells two dUTPase isoforms have been described: one nuclear (DUT-N) and one mitochondrial (DUT-M), with cognate localization signals. In contrast, here we identified two additional isoforms; DUT-3 without any localization signal and DUT-4 with the same nuclear localization signal as DUT-N. Based on an RT-qPCR method for simultaneous isoform-specific quantification we analysed the relative expression patterns in 20 human cell lines of highly different origins. We found that the DUT-N isoform is expressed by far at the highest level, followed by the DUT-M and the DUT-3 isoform. A strong correlation between expression levels of DUT-M and DUT-3 suggests that these two isoforms may share the same promoter. We analysed the effect of serum starvation on the expression of dUTPase isoforms compared to non-treated cells and found that the mRNA levels of DUT-N decreased in A-549 and MDA-MB-231 cells, but not in HeLa cells. Surprisingly, upon serum starvation DUT-M and DUT-3 showed a significant increase in the expression, while the expression level of the DUT-4 isoform did not show any changes. Taken together our results indicate that the cellular dUTPase supply may also be provided in the cytoplasm and starvation stress induced expression changes are cell line dependent.
Collapse
Affiliation(s)
- Gergely Attila Rácz
- Department of Applied Biotechnology and Food Sciences, Faculty of Chemical Technology and Biotechnology, BME Budapest University of Technology and Economics, Műegyetem Rkp. 3., Budapest, 1111, Hungary.
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH Eötvös Loránd Research Network, Budapest, Hungary.
| | - Nikolett Nagy
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH Eötvös Loránd Research Network, Budapest, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, 1117 Budapest Pázmány Péter Sétány 1/C, Budapest, Hungary
| | - György Várady
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH Eötvös Loránd Research Network, Budapest, Hungary
| | - József Tóvári
- Department of Experimental Pharmacology, National Institute of Oncology, Ráth Gy. U. 7-9, Budapest, 1122, Hungary
| | - Ágota Apáti
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH Eötvös Loránd Research Network, Budapest, Hungary
| | - Beáta G Vértessy
- Department of Applied Biotechnology and Food Sciences, Faculty of Chemical Technology and Biotechnology, BME Budapest University of Technology and Economics, Műegyetem Rkp. 3., Budapest, 1111, Hungary.
- Institute of Enzymology, Research Centre for Natural Sciences, ELKH Eötvös Loránd Research Network, Budapest, Hungary.
| |
Collapse
|
4
|
Zoghlami M, Oueslati M, Basharat Z, Sadfi-Zouaoui N, Messaoudi A. Inhibitor Assessment against the LpxC Enzyme of Antibiotic-resistant Acinetobacter baumannii Using Virtual Screening, Dynamics Simulation, and in vitro Assays. Mol Inform 2023; 42:e2200061. [PMID: 36289054 DOI: 10.1002/minf.202200061] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 10/26/2022] [Indexed: 11/07/2022]
Abstract
BACKGROUND Bacterial resistance is currently a significant global public health problem. Acinetobacter baumannii has been ranked in the list of the World Health Organization as the most critical and priority pathogen for which new antibiotics are urgently needed. In this context, computational methods play a central role in the modern drug discovery process. The purpose of the current study was to identify new potential therapeutic molecules to neutralize MDR A. baumannii bacteria. METHODS A total of 3686 proteins retrieved from the A. baumannii proteome were subjected to subtractive proteomic analysis to narrow down the spectrum of drug targets. The SWISS-MODEL server was used to perform a 3D homology model of the selected target protein. The SAVES server was used to evaluate the overall quality of the model. A dataset of 74500 analogues retrieved from the PubChem database was docked with LpxC using the AutoDock software. RESULTS In this study, we predicted a putative new inhibitor for the Lpxc enzyme of A. baumannii. The LpxC enzyme was selected as the most appropriate drug target for A. baumannii. According to the virtual screening results, N-[(2S)-3-amino-1-(hydroxyamino)-1-oxopropan-2-yl]-4-(4-bromophenyl) benzamide (CS250) could be a promising drug candidate targeting the LpxC enzyme. This molecule shows polar interactions with six amino acids and non-polar interactions with eight other residues. In vitro experimental validation was performed through the inhibition assay. CONCLUSION To the best of our knowledge, this is the first study that suggests CS250 as a promising inhibitory molecule that can be exploited to target this gram-negative pathogen.
Collapse
Affiliation(s)
- Manel Zoghlami
- Laboratoire de Mycologie, Pathologies et Biomarqueurs (LR16ES05), Département de Biologie, Université de Tunis-El Manar, 2092, Tunis, Tunisia
| | - Maroua Oueslati
- Laboratoire de Mycologie, Pathologies et Biomarqueurs (LR16ES05), Département de Biologie, Université de Tunis-El Manar, 2092, Tunis, Tunisia
| | - Zarrin Basharat
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS University of Karachi, 75270, Karachi, Pakistan
| | - Najla Sadfi-Zouaoui
- Laboratoire de Mycologie, Pathologies et Biomarqueurs (LR16ES05), Département de Biologie, Université de Tunis-El Manar, 2092, Tunis, Tunisia
| | - Abdelmonaem Messaoudi
- Laboratoire de Mycologie, Pathologies et Biomarqueurs (LR16ES05), Département de Biologie, Université de Tunis-El Manar, 2092, Tunis, Tunisia.,Higher Institute of Biotechnology of Beja, Jendouba University, Habib Bourguiba Street, 9000, Beja, Tunisia
| |
Collapse
|
5
|
Sato D, Hartuti ED, Inaoka DK, Sakura T, Amalia E, Nagahama M, Yoshioka Y, Tsuji N, Nozaki T, Kita K, Harada S, Matsubayashi M, Shiba T. Structural and Biochemical Features of Eimeria tenella Dihydroorotate Dehydrogenase, a Potential Drug Target. Genes (Basel) 2020; 11:genes11121468. [PMID: 33297567 PMCID: PMC7762340 DOI: 10.3390/genes11121468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 12/23/2022] Open
Abstract
Dihydroorotate dehydrogenase (DHODH) is a mitochondrial monotopic membrane protein that plays an essential role in the pyrimidine de novo biosynthesis and electron transport chain pathways. In Eimeria tenella, an intracellular apicomplexan parasite that causes the most severe form of chicken coccidiosis, the activity of pyrimidine salvage pathway at the intracellular stage is negligible and it relies on the pyrimidine de novo biosynthesis pathway. Therefore, the enzymes of the de novo pathway are considered potential drug target candidates for the design of compounds with activity against this parasite. Although, DHODHs from E. tenella (EtDHODH), Plasmodium falciparum (PfDHODH), and human (HsDHODH) show distinct sensitivities to classical DHODH inhibitors, in this paper, we identify ferulenol as a potent inhibitor of both EtDHODH and HsDHODH. Additionally, we report the crystal structures of EtDHODH and HsDHODH in the absence and presence of ferulenol. Comparison of these enzymes showed that despite similar overall structures, the EtDHODH has a long insertion in the N-terminal helix region that assumes a disordered configuration. In addition, the crystal structures revealed that the ferulenol binding pocket of EtDHODH is larger than that of HsDHODH. These differences can be explored to accelerate structure-based design of inhibitors specifically targeting EtDHODH.
Collapse
Affiliation(s)
- Dan Sato
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; (D.S.); (M.N.); (Y.Y.); (S.H.)
| | - Endah Dwi Hartuti
- Department of Parasitology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan;
| | - Daniel Ken Inaoka
- Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan;
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan;
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (E.A.); (T.N.)
- Correspondence: (D.K.I.); (T.S.); Tel.: +81-95-819-7230 (D.K.I.); Tel./Fax: +81-75-724-7541 (T.S.)
| | - Takaya Sakura
- Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan;
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan;
| | - Eri Amalia
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (E.A.); (T.N.)
| | - Madoka Nagahama
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; (D.S.); (M.N.); (Y.Y.); (S.H.)
| | - Yukina Yoshioka
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; (D.S.); (M.N.); (Y.Y.); (S.H.)
| | - Naotoshi Tsuji
- Department of Parasitology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan;
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (E.A.); (T.N.)
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan;
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (E.A.); (T.N.)
- Department of Host-Defense Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Shigeharu Harada
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; (D.S.); (M.N.); (Y.Y.); (S.H.)
| | - Makoto Matsubayashi
- Division of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku Orai Kita, Izumisano, Osaka 598-8531, Japan;
| | - Tomoo Shiba
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; (D.S.); (M.N.); (Y.Y.); (S.H.)
- Correspondence: (D.K.I.); (T.S.); Tel.: +81-95-819-7230 (D.K.I.); Tel./Fax: +81-75-724-7541 (T.S.)
| |
Collapse
|
6
|
Pérez-Moreno G, Sánchez-Carrasco P, Ruiz-Pérez LM, Johansson NG, Müller S, Baragaña B, Hampton SE, Gilbert IH, Kaiser M, Sarkar S, Pandurangan T, Kumar V, González-Pacanowska D. Validation of Plasmodium falciparum dUTPase as the target of 5'-tritylated deoxyuridine analogues with anti-malarial activity. Malar J 2019; 18:392. [PMID: 31796083 PMCID: PMC6889535 DOI: 10.1186/s12936-019-3025-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 11/21/2019] [Indexed: 11/24/2022] Open
Abstract
Background Malaria remains as a major global problem, being one of the infectious diseases that engender highest mortality across the world. Due to the appearance of resistance and the lack of an effective vaccine, the search of novel anti-malarials is required. Deoxyuridine 5′-triphosphate nucleotido-hydrolase (dUTPase) is responsible for the hydrolysis of dUTP to dUMP within the parasite and has been proposed as an essential step in pyrimidine metabolism by providing dUMP for thymidylate biosynthesis. In this work, efforts to validate dUTPase as a drug target in Plasmodium falciparum are reported. Methods To investigate the role of PfdUTPase in cell survival different strategies to generate knockout mutants were used. For validation of PfdUTPase as the intracellular target of four inhibitors of the enzyme, mutants overexpressing PfdUTPase and HsdUTPase were created and the IC50 for each cell line with each compound was determined. The effect of these compounds on dUTP and dTTP levels from P. falciparum was measured using a DNA polymerase assay. Detailed localization studies by indirect immunofluorescence microscopy and live cell imaging were also performed using a cell line overexpressing a Pfdut-GFP fusion protein. Results Different attempts of disruption of the dut gene of P. falciparum were unsuccessful while a 3′ replacement construct could recombine correctly in the locus suggesting that the enzyme is essential. The four 5′-tritylated deoxyuridine analogues described are potent inhibitors of the P. falciparum dUTPase and exhibit antiplasmodial activity. Overexpression of the Plasmodium and human enzymes conferred resistance against selective compounds, providing chemical validation of the target and confirming that indeed dUTPase inhibition is involved in anti-malarial activity. In addition, incubation with these inhibitors was associated with a depletion of the dTTP pool corroborating the central role of dUTPase in dTTP synthesis. PfdUTPase is mainly localized in the cytosol. Conclusion These results strongly confirm the pivotal and essential role of dUTPase in pyrimidine biosynthesis of P. falciparum intraerythrocytic stages.
Collapse
Affiliation(s)
- Guiomar Pérez-Moreno
- Instituto de Parasitología y Biomedicina López-Neyra. Consejo Superior de Investigaciones Científicas. Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, s/n 18016-Armilla, Granada, Spain
| | - Paula Sánchez-Carrasco
- Instituto de Parasitología y Biomedicina López-Neyra. Consejo Superior de Investigaciones Científicas. Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, s/n 18016-Armilla, Granada, Spain
| | - Luis Miguel Ruiz-Pérez
- Instituto de Parasitología y Biomedicina López-Neyra. Consejo Superior de Investigaciones Científicas. Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, s/n 18016-Armilla, Granada, Spain
| | | | - Sylke Müller
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, 120 University Place, Glasgow, G12 8TA, UK
| | - Beatriz Baragaña
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Shahienaz Emma Hampton
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Ian Hugh Gilbert
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Marcel Kaiser
- Swiss Tropical and Public Health Institute (Swiss TPH), Socinstrasse 57, 4051, Basel, Switzerland.,University of Basel, Petersplatz 1, 4003, Basel, Switzerland
| | - Sandipan Sarkar
- Syngene International Ltd, Biocon Park, SEZ, Bommasandra Industrial Area - Phase-IV Bommasandra-Jigani Link Road, Bangalore, 560 099, India
| | - Thiyagamurthy Pandurangan
- Syngene International Ltd, Biocon Park, SEZ, Bommasandra Industrial Area - Phase-IV Bommasandra-Jigani Link Road, Bangalore, 560 099, India
| | - Vijeesh Kumar
- Syngene International Ltd, Biocon Park, SEZ, Bommasandra Industrial Area - Phase-IV Bommasandra-Jigani Link Road, Bangalore, 560 099, India
| | - Dolores González-Pacanowska
- Instituto de Parasitología y Biomedicina López-Neyra. Consejo Superior de Investigaciones Científicas. Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, s/n 18016-Armilla, Granada, Spain.
| |
Collapse
|
7
|
Rácz GA, Nagy N, Gál Z, Pintér T, Hiripi L, Vértessy BG. Evaluation of critical design parameters for RT-qPCR-based analysis of multiple dUTPase isoform genes in mice. FEBS Open Bio 2019; 9:1153-1170. [PMID: 31077566 PMCID: PMC6551494 DOI: 10.1002/2211-5463.12654] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 05/01/2019] [Accepted: 05/10/2019] [Indexed: 11/09/2022] Open
Abstract
The coupling of nucleotide biosynthesis and genome integrity plays an important role in ensuring faithful maintenance and transmission of genetic information. The enzyme dUTPase is a prime example of such coupling, as it generates dUMP for thymidylate biosynthesis and removes dUTP for synthesis of uracil-free DNA. Despite its significant role, the expression patterns of dUTPase isoforms in animals have not yet been described. Here, we developed a detailed optimization procedure for RT-qPCR-based isoform-specific analysis of dUTPase expression levels in various organs of adult mice. Primer design, optimal annealing temperature, and primer concentrations were specified for both nuclear and mitochondrial dUTPase isoforms, as well as two commonly used reference genes, GAPDH and PPIA. The linear range of the RNA concentration for the reverse transcription reaction was determined. The PCR efficiencies were calculated using serial dilutions of cDNA. Our data indicate that organs involved in lymphocyte production, as well as reproductive organs, are characterized by high levels of expression of the nuclear dUTPase isoform. On the other hand, we observed that expression of the mitochondrial dUTPase isoform is considerably increased in heart, kidney, and ovary. Despite the differences in expression levels among the various organs, we also found that the mitochondrial dUTPase isoform shows a much more uniform expression pattern as compared to the reference genes GAPDH and PPIA.
Collapse
Affiliation(s)
- Gergely A Rácz
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Budapest, Hungary.,Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Nikolett Nagy
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Budapest, Hungary.,Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| | - Zoltán Gál
- Department of Animal Biotechnology, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, Gödöllő, Hungary.,Faculty of Agricultural and Environmental Science, Szent István University, Gödöllő, Hungary
| | - Tímea Pintér
- Department of Animal Biotechnology, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, Gödöllő, Hungary
| | - László Hiripi
- Department of Animal Biotechnology, Agricultural Biotechnology Institute, National Agricultural Research and Innovation Centre, Gödöllő, Hungary
| | - Beáta G Vértessy
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Budapest, Hungary.,Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, Hungary
| |
Collapse
|