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PEI-Mediated Transient Transfection of High Five Cells at Bioreactor Scale for HIV-1 VLP Production. NANOMATERIALS 2020; 10:nano10081580. [PMID: 32806511 PMCID: PMC7466501 DOI: 10.3390/nano10081580] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/20/2020] [Accepted: 08/07/2020] [Indexed: 12/25/2022]
Abstract
High Five cells are an excellent host for the production of virus-like particles (VLPs) with the baculovirus expression vector system (BEVS). However, the concurrent production of high titers of baculovirus hinder the purification of these nanoparticles due to similarities in their physicochemical properties. In this study, first a transient gene expression (TGE) method based on the transfection reagent polyethylenimine (PEI) is optimized for the production of HIV-1 VLPs at shake flask level. Furthermore, VLP production by TGE in High Five cells is successfully demonstrated at bioreactor scale, resulting in a higher maximum viable cell concentration (5.1 × 106 cell/mL), the same transfection efficiency and a 1.8-fold increase in Gag-eGFP VLP production compared to shake flasks. Metabolism analysis of High Five cells indicates a reduction in the consumption of the main metabolites with respect to non-transfected cell cultures, and an increase in the uptake rate of several amino acids when asparagine is depleted. Quality assessment by nanoparticle tracking analysis and flow virometry of the VLPs produced shows an average size of 100–200 nm, in agreement with immature HIV-1 viruses reported in the literature. Overall, this work demonstrates that the High Five/TGE system is a suitable approach for the production of VLP-based vaccine candidates and other recombinant proteins.
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Mishima Y, Brueckner L, Takahashi S, Kawakami T, Otani J, Shinohara A, Takeshita K, Garvilles RG, Watanabe M, Sakai N, Takeshima H, Nachtegael C, Nishiyama A, Nakanishi M, Arita K, Nakashima K, Hojo H, Suetake I. Enhanced processivity of Dnmt1 by monoubiquitinated histone H3. Genes Cells 2019; 25:22-32. [DOI: 10.1111/gtc.12732] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 10/30/2019] [Accepted: 10/30/2019] [Indexed: 12/30/2022]
Affiliation(s)
- Yuichi Mishima
- Laboratory of Epigenetics Institute for Protein Research Osaka University Suita Japan
| | - Laura Brueckner
- Laboratory of Epigenetics Institute for Protein Research Osaka University Suita Japan
| | - Saori Takahashi
- Laboratory of Epigenetics Institute for Protein Research Osaka University Suita Japan
| | - Toru Kawakami
- Laboratory of Organic Chemistry Institute for Protein Research Osaka University Suita Japan
| | - Junji Otani
- Laboratory of Epigenetics Institute for Protein Research Osaka University Suita Japan
| | - Akira Shinohara
- Laboratory of Genome‐Chromosome Function Institute for Protein Research Osaka University Suita Japan
| | | | | | - Mikio Watanabe
- Center for Twin Research Graduate School of Medicine Osaka University Suita Japan
| | - Norio Sakai
- Center for Twin Research Graduate School of Medicine Osaka University Suita Japan
| | - Hideyuki Takeshima
- Division of Epigenomics National Cancer Center Research Institute Tokyo Japan
| | - Charlotte Nachtegael
- Laboratory of Epigenetics Institute for Protein Research Osaka University Suita Japan
- Interuniversity Institute of Bioinformatics in Brussels Universite Libre de Bruxelles‐Vrije Universiteit Brussel Brussels Belgium
| | - Atsuya Nishiyama
- Division of Cancer Cell Biology The Institute of Medical Science The University of Tokyo Tokyo Japan
| | - Makoto Nakanishi
- Division of Cancer Cell Biology The Institute of Medical Science The University of Tokyo Tokyo Japan
| | - Kyohei Arita
- Graduate School of Medical Life Science Yokohama City University Yokohama Japan
| | - Kinichi Nakashima
- Department of Stem Cell Biology and Medicine Graduate School of Medical Sciences Kyushu University Fukuoka Japan
| | - Hironobu Hojo
- Laboratory of Organic Chemistry Institute for Protein Research Osaka University Suita Japan
| | - Isao Suetake
- Laboratory of Epigenetics Institute for Protein Research Osaka University Suita Japan
- Center for Twin Research Graduate School of Medicine Osaka University Suita Japan
- College of Nutrition Koshien University Takarazuka Japan
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Mishima Y, Brueckner L, Takahashi S, Kawakami T, Arita K, Oka S, Otani J, Hojo H, Shirakawa M, Shinohara A, Watanabe M, Suetake I. RFTS-dependent negative regulation of Dnmt1 by nucleosome structure and histone tails. FEBS J 2017; 284:3455-3469. [DOI: 10.1111/febs.14205] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 07/07/2017] [Accepted: 08/17/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Yuichi Mishima
- Laboratory of Epigenetics; Institute for Protein Research; Osaka University; Suita Japan
| | - Laura Brueckner
- Laboratory of Epigenetics; Institute for Protein Research; Osaka University; Suita Japan
| | - Saori Takahashi
- Laboratory of Epigenetics; Institute for Protein Research; Osaka University; Suita Japan
| | - Toru Kawakami
- Laboratory of Organic Chemistry; Institute for Protein Research; Osaka University; Suita Japan
| | - Kyohei Arita
- Division of Macromolecular Crystallography; Graduate School of Nanobioscience; Yokohama City University; Japan
| | - Shota Oka
- Laboratory of Epigenetics; Institute for Protein Research; Osaka University; Suita Japan
| | - Junji Otani
- Laboratory of Epigenetics; Institute for Protein Research; Osaka University; Suita Japan
| | - Hironobu Hojo
- Laboratory of Organic Chemistry; Institute for Protein Research; Osaka University; Suita Japan
| | - Masahiro Shirakawa
- Department of Molecular Engineering; Graduate School of Engineering; Kyoto University; Japan
- CREST; Japan Science and Technology Agency; Saitama Japan
| | - Akira Shinohara
- Laboratory of Genome-Chromosome Functions; Institute for Protein Research; Osaka University; Suita Japan
| | - Mikio Watanabe
- Center for Twin Research; Graduate School of Medicine; Osaka University; Suita Japan
| | - Isao Suetake
- Laboratory of Epigenetics; Institute for Protein Research; Osaka University; Suita Japan
- CREST; Japan Science and Technology Agency; Saitama Japan
- Center for Twin Research; Graduate School of Medicine; Osaka University; Suita Japan
- College of Nutrition; Koshien University; Takarazuka Japan
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Mitsudome T, Mon H, Xu J, Li Z, Lee JM, Patil AA, Masuda A, Iiyama K, Morokuma D, Kusakabe T. Biochemical characterization of maintenance DNA methyltransferase DNMT-1 from silkworm, Bombyx mori. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2015; 58:55-65. [PMID: 25623240 DOI: 10.1016/j.ibmb.2015.01.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 01/13/2015] [Accepted: 01/15/2015] [Indexed: 06/04/2023]
Abstract
DNA methylation is an important epigenetic mechanism involved in gene expression of vertebrates and invertebrates. In general, DNA methylation profile is established by de novo DNA methyltransferases (DNMT-3A, -3B) and maintainance DNA methyltransferase (DNMT-1). DNMT-1 has a strong substrate preference for hemimethylated DNA over the unmethylated one. Because the silkworm genome lacks an apparent homologue of de novo DNMT, it is still unclear that how silkworm chromosome establishes and maintains its DNA methylation profile. As the first step to unravel this enigma, we purified recombinant BmDNMT-1 using baculovirus expression system and characterized its DNA-binding and DNA methylation activity. We found that the BmDNMT-1 preferentially methylates hemimethylated DNA despite binding to both unmethylated and hemimethylated DNA. Interestingly, BmDNMT-1 formed a complex with DNA in the presence or absence of methyl group donor, S-Adenosylmethionine (AdoMet) and the AdoMet-dependent complex formation was facilitated by Zn(2+) and Mn(2+). Our results provide clear evidence that BmDNMT-1 retained the function as maintenance DNMT but its sensitivity to metal ions is different from mammalian DNMT-1.
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Affiliation(s)
- Takumi Mitsudome
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Fukuoka, Japan
| | - Hiroaki Mon
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Fukuoka, Japan
| | - Jian Xu
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Fukuoka, Japan
| | - Zhiqing Li
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Fukuoka, Japan
| | - Jae Man Lee
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Fukuoka, Japan
| | - Anandrao Ashok Patil
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Fukuoka, Japan
| | - Atsushi Masuda
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Fukuoka, Japan
| | - Kazuhiro Iiyama
- Laboratory of Insect Pathology and Microbial Control, Institute of Biological Control, Faculty of Agriculture, Graduate School, Kyushu University, Fukuoka, Japan
| | - Daisuke Morokuma
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Fukuoka, Japan
| | - Takahiro Kusakabe
- Laboratory of Insect Genome Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Fukuoka, Japan.
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Berkyurek AC, Suetake I, Arita K, Takeshita K, Nakagawa A, Shirakawa M, Tajima S. The DNA methyltransferase Dnmt1 directly interacts with the SET and RING finger-associated (SRA) domain of the multifunctional protein Uhrf1 to facilitate accession of the catalytic center to hemi-methylated DNA. J Biol Chem 2013; 289:379-86. [PMID: 24253042 DOI: 10.1074/jbc.m113.523209] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dnmt1 is responsible for the maintenance DNA methylation during replication to propagate methylation patterns to the next generation. The replication foci targeting sequence (RFTS), which plugs the catalytic pocket, is necessary for recruitment of Dnmt1 to the replication site. In the present study we found that the DNA methylation activity of Dnmt1 was DNA length-dependent and scarcely methylated 12-bp short hemi-methylated DNA. Contrarily, the RFTS-deleted Dnmt1 and Dnmt1 mutants that destroyed the hydrogen bonds between the RFTS and catalytic domain showed significant DNA methylation activity even toward 12-bp hemi-methylated DNA. The DNA methylation activity of the RFTS-deleted Dnmt1 toward 12-bp hemi-methylated DNA was strongly inhibited on the addition of RFTS, but to a lesser extent by Dnmt1 harboring the mutations that impair the hydrogen bond formation. The SRA domain of Uhrf1, which is a prerequisite factor for maintenance methylation and selectively binds to hemi-methylated DNA, stimulated the DNA methylation activity of Dnmt1. The SRA to Dnmt1 concentration ratio was the determinant for the maximum stimulation. In addition, a mutant SRA, which had lost the DNA binding activity but was able to bind to Dnmt1, stimulated the DNA methylation activity of Dnmt1. The results indicate that the DNA methylation activity of Dnmt1 was stimulated on the direct interaction of the SRA and Dnmt1. The SRA facilitated acceptance of the 12-bp fluorocytosine-containing DNA by the catalytic center. We propose that the SRA removes the RFTS plug from the catalytic pocket to facilitate DNA acceptance by the catalytic center.
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Affiliation(s)
- Ahmet Can Berkyurek
- From the Institute for Protein Research, Osaka University, 3-2, Yamadaoka, Suita, Osaka 565-0871, Japan
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van Bemmel DM, Brank AS, Eritja R, Marquez VE, Christman JK. DNA (Cytosine-C5) methyltransferase inhibition by oligodeoxyribonucleotides containing 2-(1H)-pyrimidinone (zebularine aglycon) at the enzymatic target site. Biochem Pharmacol 2009; 78:633-41. [PMID: 19467223 DOI: 10.1016/j.bcp.2009.05.017] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2009] [Revised: 05/15/2009] [Accepted: 05/15/2009] [Indexed: 11/16/2022]
Abstract
Aberrant cytosine methylation in promoter regions leads to gene silencing associated with cancer progression. A number of DNA methyltransferase inhibitors are known to reactivate silenced genes; including 5-azacytidine and 2-(1H)-pyrimidinone riboside (zebularine). Zebularine is a more stable, less cytotoxic inhibitor compared to 5-azacytidine. To determine the mechanistic basis for this difference, we carried out a detailed comparisons of the interaction between purified DNA methyltransferases and oligodeoxyribonucleotides (ODNs) containing either 5-azacytosine or 2-(1H)-pyrimidinone in place of the cytosine targeted for methylation. When incorporated into small ODNs, the rate of C5 DNA methyltransferase inhibition by both nucleosides is essentially identical. However, the stability and reversibility of the enzyme complex in the absence and presence of cofactor differs. 5-Azacytosine ODNs form complexes with C5 DNA methyltransferases that are irreversible when the 5-azacytosine ring is intact. ODNs containing 2-(1H)-pyrimidinone at the enzymatic target site are competitive inhibitors of both prokaryotic and mammalian DNA C5 methyltransferases. We determined that the ternary complexes between the enzymes, 2-(1H)-pyrimidinone inhibitor, and the cofactor S-adenosyl methionine are maintained through the formation of a reversible covalent interaction. The differing stability and reversibility of the covalent bonds may partially account for the observed differences in cytotoxicity between zebularine and 5-azacytidine inhibitors.
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Affiliation(s)
- Dana M van Bemmel
- Department of Biochemistry and Molecular Biology, Omaha, NE 68198-5870, USA.
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Baculovirus expression and bioactivity of a soluble 140kDa extracellular cleavage fragment of L1 neural cell adhesion molecule. Protein Expr Purif 2008; 57:172-9. [DOI: 10.1016/j.pep.2007.10.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2007] [Revised: 10/08/2007] [Accepted: 10/11/2007] [Indexed: 11/21/2022]
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Fang MZ, Chen D, Sun Y, Jin Z, Christman JK, Yang CS. Reversal of hypermethylation and reactivation of p16INK4a, RARbeta, and MGMT genes by genistein and other isoflavones from soy. Clin Cancer Res 2005; 11:7033-41. [PMID: 16203797 DOI: 10.1158/1078-0432.ccr-05-0406] [Citation(s) in RCA: 263] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE We have previously shown the reactivation of some methylation-silenced genes in cancer cells by (-)-epigallocatechin-3-gallate, the major polyphenol from green tea. To determine whether other polyphenolic compounds have similar activities, we studied the effects of soy isoflavones on DNA methylation. EXPERIMENTAL DESIGN Enzyme assay was used to determine the inhibitory effect of genistein on DNA methyltransferase activity in nuclear extracts and purified recombinant enzyme. Methylation-specific PCR and quantitative real-time PCR were employed to examine the DNA methylation and gene expression status of retinoic acid receptor beta (RARbeta), p16INK4a, and O6-methylguanine methyltransferase (MGMT) in KYSE 510 esophageal squamous cell carcinoma cells treated with genistein alone or in combination with trichostatin, sulforaphane, or 2'-deoxy-5-aza-cytidine (5-aza-dCyd). RESULTS Genistein (2-20 micromol/L) reversed DNA hypermethylation and reactivated RARbeta, p16INK4a, and MGMT in KYSE 510 cells. Genistein also inhibited cell growth at these concentrations. Reversal of DNA hypermethylation and reactivation of RARbeta by genistein were also observed in KYSE 150 cells and prostate cancer LNCaP and PC3 cells. Genistein (20-50 micromol/L) dose-dependently inhibited DNA methyltransferase activity, showing substrate- and methyl donor-dependent inhibition. Biochanin A and daidzein were less effective in inhibiting DNA methyltransferase activity, in reactivating RARbeta, and in inhibiting cancer cell growth. In combination with trichostatin, sulforaphane, or 5-aza-dCyd, genistein enhanced reactivation of these genes and inhibition of cell growth. CONCLUSIONS These results indicate that genistein and related soy isoflavones reactivate methylation-silenced genes, partially through a direct inhibition of DNA methyltransferase, which may contribute to the chemopreventive activity of dietary isoflavones.
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Affiliation(s)
- Ming Zhu Fang
- Susan Lehman Cullman Laboratory for Cancer Research, Department of Chemical Biology, Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854-8020, USA
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Vilkaitis G, Suetake I, Klimasauskas S, Tajima S. Processive Methylation of Hemimethylated CpG Sites by Mouse Dnmt1 DNA Methyltransferase. J Biol Chem 2005; 280:64-72. [PMID: 15509558 DOI: 10.1074/jbc.m411126200] [Citation(s) in RCA: 146] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA methyltransferase Dnmt1 ensures clonal transmission of lineage-specific DNA methylation patterns in a mammalian genome during replication. Dnmt1 is targeted to replication foci, interacts with PCNA, and favors methylating the hemimethylated form of CpG sites. To understand the underlying mechanism of its maintenance function, we purified recombinant forms of full-length Dnmt1, a truncated form of Dnmt1-(291-1620) lacking the binding sites for PCNA and DNA and examined their processivity using a series of long unmethylated and hemimethylated DNA substrates. Direct analysis of methylation patterns using bisulfite-sequencing and hairpin-PCR techniques demonstrated that full-length Dnmt1 methylates hemimethylated DNA with high processivity and a fidelity of over 95%, but unmethylated DNA with much less processivity. The truncated form of Dnmt1 showed identical properties to full-length Dnmt1 indicating that the N-terminal 290-amino acid residue region of Dnmt1 is not required for preferential activity toward hemimethylated sites or for processivity of the enzyme. Remarkably, our analyses also revealed that Dnmt1 methylates hemimethylated CpG sites on one strand of double-stranded DNA during a single processive run. Our findings suggest that these inherent enzymatic properties of Dnmt1 play an essential role in the faithful and efficient maintenance of methylation patterns in the mammalian genome.
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Affiliation(s)
- Giedrius Vilkaitis
- Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan
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Christman JK. 5-Azacytidine and 5-aza-2'-deoxycytidine as inhibitors of DNA methylation: mechanistic studies and their implications for cancer therapy. Oncogene 2002; 21:5483-95. [PMID: 12154409 DOI: 10.1038/sj.onc.1205699] [Citation(s) in RCA: 1016] [Impact Index Per Article: 46.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
5-Azacytidine was first synthesized almost 40 years ago. It was demonstrated to have a wide range of anti-metabolic activities when tested against cultured cancer cells and to be an effective chemotherapeutic agent for acute myelogenous leukemia. However, because of 5-azacytidine's general toxicity, other nucleoside analogs were favored as therapeutics. The finding that 5-azacytidine was incorporated into DNA and that, when present in DNA, it inhibited DNA methylation, led to widespread use of 5-azacytidine and 5-aza-2'-deoxycytidine (Decitabine) to demonstrate the correlation between loss of methylation in specific gene regions and activation of the associated genes. There is now a revived interest in the use of Decitabine as a therapeutic agent for cancers in which epigenetic silencing of critical regulatory genes has occurred. Here, the current status of our understanding of the mechanism(s) by which 5-azacytosine residues in DNA inhibit DNA methylation is reviewed with an emphasis on the interactions of these residues with bacterial and mammalian DNA (cytosine-C5) methyltransferases. The implications of these mechanistic studies for development of less toxic inhibitors of DNA methylation are discussed.
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Affiliation(s)
- Judith K Christman
- Department of Biochemistry and Molecular Biology and UNMC/Eppley Cancer Center, University of Nebraska Medical Center, 984525 University Medical Center, Omaha, Nebraska, NE 68198-4525, USA.
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