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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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Massender E, Oliveira HR, Brito LF, Maignel L, Jafarikia M, Baes CF, Sullivan B, Schenkel FS. Genome-wide association study for milk production and conformation traits in Canadian Alpine and Saanen dairy goats. J Dairy Sci 2023; 106:1168-1189. [PMID: 36526463 DOI: 10.3168/jds.2022-22223] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022]
Abstract
Increasing the productivity of Canadian dairy goats is critical to the competitiveness of the sector; however, little is known about the underlying genetic architecture of economically important traits in these populations. Consequently, the objectives of this study were as follows: (1) to perform a single-step GWAS for milk production traits (milk, protein, and fat yields, and protein and fat percentages in first and later lactations) and conformation traits (body capacity, dairy character, feet and legs, fore udder, general appearance, rear udder, suspensory ligament, and teats) in the Canadian Alpine and Saanen breeds; and (2) to identify positional and functional candidate genes related to these traits. The data available for analysis included 305-d milk production records for 6,409 Alpine and 3,434 Saanen does in first lactation and 5,827 Alpine and 2,632 Saanen does in later lactations; as well as linear type conformation records for 5,158 Alpine and 2,342 Saanen does. Genotypes were available for 833 Alpine and 874 Saanen animals. Both single-breed and multiple-breed GWAS were performed using single-trait animal models. Positional and functional candidate genes were then identified in downstream analyses. The GWAS identified 189 unique SNP that were significant at the chromosomal level, corresponding to 271 unique positional candidate genes within 50 kb up- and downstream, across breeds and traits. This study provides evidence for the economic importance of several candidate genes (e.g., CSN1S1, CSN2, CSN1S2, CSN3, DGAT1, and ZNF16) in the Canadian Alpine and Saanen populations that have been previously reported in other dairy goat populations. Moreover, several novel positional and functional candidate genes (e.g., RPL8, DCK, and MOB1B) were also identified. Overall, the results of this study have provided greater insight into the genetic architecture of milk production and conformation traits in the Canadian Alpine and Saanen populations. Greater understanding of these traits will help to improve dairy goat breeding programs.
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Affiliation(s)
- Erin Massender
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.
| | - Hinayah R Oliveira
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Luiz F Brito
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Laurence Maignel
- Canadian Centre for Swine Improvement Inc., Ottawa, ON, K1A 0C6, Canada
| | - Mohsen Jafarikia
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Canadian Centre for Swine Improvement Inc., Ottawa, ON, K1A 0C6, Canada
| | - Christine F Baes
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - Brian Sullivan
- Canadian Centre for Swine Improvement Inc., Ottawa, ON, K1A 0C6, Canada
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
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Makurat S, Cournia Z, Rak J. Inactive-to-Active Transition of Human Thymidine Kinase 1 Revealed by Molecular Dynamics Simulations. J Chem Inf Model 2022; 62:142-149. [PMID: 34919400 PMCID: PMC8757434 DOI: 10.1021/acs.jcim.1c01157] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Indexed: 11/28/2022]
Abstract
Despite its importance in the nucleoside (and nucleoside prodrug) metabolism, the structure of the active conformation of human thymidine kinase 1 (hTK1) remains elusive. We perform microsecond molecular dynamics simulations of the inactive enzyme form bound to a bisubstrate inhibitor that was shown experimentally to activate another TK1-like kinase, Thermotoga maritima TK (TmTK). Our results are in excellent agreement with the experimental findings for the TmTK closed-to-open state transition. We show that the inhibitor induces an increase of the enzyme radius of gyration due to the expansion on one of the dimer interfaces; the structural changes observed, including the active site pocket volume increase and the decrease in the monomer-monomer buried surface area and of the number of hydrogen bonds (as compared to the inactive enzyme control simulation), indicate that the catalytically competent (open) conformation of hTK1 can be assumed in the presence of an activating ligand.
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Affiliation(s)
- Samanta Makurat
- Faculty
of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Zoe Cournia
- Biomedical
Research Foundation, Academy of Athens, 4 Soranou Ephessiou, 11527 Athens, Greece
| | - Janusz Rak
- Faculty
of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
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Abstract
We here described a three-step multi-enzymatic reaction for the one-pot synthesis of vidarabine 5′-monophosphate (araA-MP), an antiviral drug, using arabinosyluracil (araU), adenine (Ade), and adenosine triphosphate (ATP) as precursors. To this aim, three enzymes involved in the biosynthesis of nucleosides and nucleotides were used in a cascade mode after immobilization: uridine phosphorylase from Clostridium perfringens (CpUP), a purine nucleoside phosphorylase from Aeromonas hydrophila (AhPNP), and deoxyadenosine kinase from Dictyostelium discoideum (DddAK). Specifically, CpUP catalyzes the phosphorolysis of araU thus generating uracil and α-d-arabinose-1-phosphate. AhPNP catalyzes the coupling between this latter compound and Ade to form araA (vidarabine). This nucleoside becomes the substrate of DddAK, which produces the 5′-mononucleotide counterpart (araA-MP) using ATP as the phosphate donor. Reaction conditions (i.e., medium, temperature, immobilization carriers) and biocatalyst stability have been balanced to achieve the highest conversion of vidarabine 5′-monophosphate (≥95.5%). The combination of the nucleoside phosphorylases twosome with deoxyadenosine kinase in a one-pot cascade allowed (i) a complete shift in the equilibrium-controlled synthesis of the nucleoside towards the product formation; and (ii) to overcome the solubility constraints of araA in aqueous medium, thus providing a new route to the highly productive synthesis of araA-MP.
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Serra I, Ubiali D, Piškur J, Munch-Petersen B, Bavaro T, Terreni M. Immobilization of Deoxyadenosine Kinase fromDictyostelium discoideum(DddAK) and Its Application in the 5’-Phosphorylation of Arabinosyladenine and Arabinosyl-2-fluoroadenine. ChemistrySelect 2017. [DOI: 10.1002/slct.201700558] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Immacolata Serra
- Department of Drug Sciences; University of Pavia; Viale T. Taramelli 12 I-27100 Pavia Italy
- Department of Food, Environmental and Nutritional Science (DeFENS); University of Milan; Via L. Mangiagalli 25 I-20133 Milano Italy
| | - Daniela Ubiali
- Department of Drug Sciences; University of Pavia; Viale T. Taramelli 12 I-27100 Pavia Italy
- ISTM-CNR; Via C. Golgi 19 I-20133 Milano Italy
| | - Jure Piškur
- Department of Biology; Lund University; Lund 22362 Sweden
| | - Birgitte Munch-Petersen
- Department of Biology; Lund University; Lund 22362 Sweden
- Department of Science, Systems and Models; Roskilde University; Roskilde 4000 Denmark
| | - Teodora Bavaro
- Department of Drug Sciences; University of Pavia; Viale T. Taramelli 12 I-27100 Pavia Italy
| | - Marco Terreni
- Department of Drug Sciences; University of Pavia; Viale T. Taramelli 12 I-27100 Pavia Italy
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Orozco Rodriguez JM, Nesrini M, Christiansen LS, Knecht W. Expression of tomato thymidine kinase 1 by means of the baculovirus expression vector system. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2017; 35:691-698. [PMID: 27906616 DOI: 10.1080/15257770.2016.1139126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Tomato thymidine kinase 1 (ToTK1) is a deoxyribonucleoside kinase (dNK) that has been subject to study because of its potential to phosphorylate the nucleoside analogue 3-azido-2,3-dideoxythymidine (azidothymidine, AZT) equally well as its natural substrate thymidine (dThd). The combination of ToTK1 and AZT has been tested in two animal studies for its efficiency and use in suicide gene therapy for malignant glioma. The determination of the 3D structure of ToTK1 might shed light on the structure-function relationships of nucleoside activation by this enzyme and thereby show routes toward further improvement of ToTK1 and other TK1-like dNKs for suicide gene therapy. Here we report the successful expression of both full-length ToTK1 and a C-terminal truncated ToTK1 in Spodoptera frugiperda and Trichoplusia ni insect cells using the baculovirus expression vector system. This constitutes a further step on the road to determine the 3D structure of the first TK1 of plant origin, but also an enzyme with great potential for dNK-mediated suicide gene therapy.
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Affiliation(s)
| | - Mohamad Nesrini
- a Department of Biology and Lund Protein Production Platform , Lund University , Lund , Sweden
| | | | - Wolfgang Knecht
- a Department of Biology and Lund Protein Production Platform , Lund University , Lund , Sweden
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Christiansen LS, van Zanten G, Berenstein D, Lauridsen M, Kjærulff S, Søndergaard L, Munch-Petersen B. Isolation of a novel protein, P12-from adult Drosophila melanogaster that inhibits deoxyribonucleoside and protein kinase activities and activates 3'-5'- exonuclease activity. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2017; 35:699-706. [PMID: 27906621 DOI: 10.1080/15257770.2015.1131295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
We have previously found that Drosophila melanogaster only has one deoxyribonucleoside kinase, Dm-dNK, however, capable to phosphorylate all four natural deoxyribonucleosides. Dm-dNK was originally isolated from an embryonic cell line. We wanted to study the expression of Dm-dNK during development from embryonic cells to adult flies and found declining Dm-dNK activity during development and no activity in adult flies. Surprisingly, the extract from adult flies exhibited a strong inhibitory effect on deoxyribonucloside kinase activity. The dNK-inhibitor was precipitable with ammonium sulfate, and was purified to a high degree by gel-filtration as indicated by LC-MS/MS analysis. Since the inhibitor eluted from G-200 gel-filtration with a size of 10-13 kDa, we named it P12. We tested the purified fraction for specificity towards various enzymes and found that both mammalian and bacterial dNKs were inhibited, whereas there was no effect on hexokinase and pyruvate kinases and acidic phosphatase. However, when tested against cyclin B-dependent kinase, we found a strong inhibitory effect. Both with human Cdk1/CycB and S. pombe Cdc2/B-type cyclin the purified fraction from Superdex 200 that inhibited Dm-dNK, also inhibited the two protein kinases to the same degree. Furthermore, testing P12 in a DNA polymerase based assay we found that the 3'-5'-exonuclease part of the DNA polymerase (Klenow polymerase) was activated.
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Affiliation(s)
| | - Gabriella van Zanten
- a Department of Science , Systems and Models, Roskilde University , Roskilde , Denmark
| | - Dvora Berenstein
- a Department of Science , Systems and Models, Roskilde University , Roskilde , Denmark
| | - Marianne Lauridsen
- a Department of Science , Systems and Models, Roskilde University , Roskilde , Denmark
| | - Søren Kjærulff
- b Department of Biology , University of Copenhagen , Copenhagen , Denmark
| | - Leif Søndergaard
- b Department of Biology , University of Copenhagen , Copenhagen , Denmark
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Mutahir Z, Christiansen LS, Clausen AR, Berchtold MW, Gojkovic Z, Munch-Petersen B, Knecht W, Piškur J. Gene duplications and losses among vertebrate deoxyribonucleoside kinases of the non-TK1 Family. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2017; 35:677-690. [PMID: 27906638 DOI: 10.1080/15257770.2016.1143557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Deoxyribonucleoside kinases (dNKs) salvage deoxyribonucleosides (dNs) and catalyze the rate limiting step of this salvage pathway by converting dNs into corresponding monophosphate forms. These enzymes serve as an excellent model to study duplicated genes and their evolutionary history. So far, among vertebrates only four mammalian dNKs have been studied for their substrate specificity and kinetic properties. However, some vertebrates, such as fish, frogs, and birds, apparently possess a duplicated homolog of deoxycytidine kinase (dCK). In this study, we characterized a family of dCK/deoxyguanosine kinase (dGK)-like enzymes from a frog Xenopus laevis and a bird Gallus gallus. We showed that X. laevis has a duplicated dCK gene and a dGK gene, whereas G. gallus has a duplicated dCK gene but has lost the dGK gene. We cloned, expressed, purified, and subsequently determined the kinetic parameters of the dCK/dGK enzymes encoded by these genes. The two dCK enzymes in G. gallus have broader substrate specificity than their human or X. laevis counterparts. Additionally, the duplicated dCK enzyme in G. gallus might have become mitochondria. Based on our study we postulate that changing and adapting substrate specificities and subcellular localization are likely the drivers behind the evolution of vertebrate dNKs.
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Affiliation(s)
| | - Louise Slot Christiansen
- a Department of Biology , Lund University , Lund , Sweden.,e Lund Protein Production Platform, Lund University , Lund , Sweden
| | | | - Martin W Berchtold
- b Department of Biology , University of Copenhagen , Copenhagen , Denmark
| | | | - Birgitte Munch-Petersen
- a Department of Biology , Lund University , Lund , Sweden.,d Department of Science , Systems and Models, Roskilde University , Roskilde , Denmark
| | - Wolfgang Knecht
- a Department of Biology , Lund University , Lund , Sweden.,e Lund Protein Production Platform, Lund University , Lund , Sweden
| | - Jure Piškur
- a Department of Biology , Lund University , Lund , Sweden
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Lutz S, Williams E, Muthu P. Engineering Therapeutic Enzymes. DIRECTED ENZYME EVOLUTION: ADVANCES AND APPLICATIONS 2017:17-67. [DOI: 10.1007/978-3-319-50413-1_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
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10
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Slot Christiansen L, Egeblad L, Munch-Petersen B, Piškur J, Knecht W. New Variants of Tomato Thymidine Kinase 1 Selected for Increased Sensitivity of E. coli KY895 towards Azidothymidine. Cancers (Basel) 2015; 7:966-80. [PMID: 26061968 PMCID: PMC4491694 DOI: 10.3390/cancers7020819] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Revised: 05/19/2015] [Accepted: 05/27/2015] [Indexed: 11/17/2022] Open
Abstract
Nucleoside analogues (NA) are prodrugs that are phosphorylated by deoxyribonucleoside kinases (dNKs) as the first step towards a compound toxic to the cell. During the last 20 years, research around dNKs has gone into new organisms other than mammals and viruses. Newly discovered dNKs have been tested as enzymes for suicide gene therapy. The tomato thymidine kinase 1 (ToTK1) is a dNK that has been selected for its in vitro kinetic properties and then successfully been tested in vivo for the treatment of malignant glioma. We present the selection of two improved variants of ToTK1 generated by random protein engineering for suicide gene therapy with the NA azidothymidine (AZT).We describe their selection, recombinant production and a subsequent kinetic and biochemical characterization. Their improved performance in killing of E. coli KY895 is accompanied by an increase in specificity for the NA AZT over the natural substrate thymidine as well as a decrease in inhibition by dTTP, the end product of the nucleoside salvage pathway for thymidine. The understanding of the enzymatic properties improving the variants efficacy is instrumental to further develop dNKs for use in suicide gene therapy.
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Affiliation(s)
- Louise Slot Christiansen
- Department of Biology, Lund University, Lund 22362, Sweden; E-Mail:
- Lund Protein Production Platform, Lund University, Lund 22362, Sweden; E-Mail:
| | - Louise Egeblad
- Lund Protein Production Platform, Lund University, Lund 22362, Sweden; E-Mail:
| | - Birgitte Munch-Petersen
- Department of Science, Systems and Models, Roskilde University, Roskilde 4000, Denmark; E-Mail:
| | - Jure Piškur
- Department of Biology, Lund University, Lund 22362, Sweden; E-Mail:
| | - Wolfgang Knecht
- Department of Biology, Lund University, Lund 22362, Sweden; E-Mail:
- Lund Protein Production Platform, Lund University, Lund 22362, Sweden; E-Mail:
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