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Horiuchi Y, Laskaratou D, Sliwa M, Ruckebusch C, Hatori K, Mizuno H, Hotta JI. Frame-Insensitive Expression Cloning of Fluorescent Protein from Scolionema suvaense. Int J Mol Sci 2018; 19:ijms19020371. [PMID: 29373508 PMCID: PMC5855593 DOI: 10.3390/ijms19020371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 01/15/2018] [Accepted: 01/24/2018] [Indexed: 11/16/2022] Open
Abstract
Expression cloning from cDNA is an important technique for acquiring genes encoding novel fluorescent proteins. However, the probability of in-frame cDNA insertion following the first start codon of the vector is normally only 1/3, which is a cause of low cloning efficiency. To overcome this issue, we developed a new expression plasmid vector, pRSET-TriEX, in which transcriptional slippage was induced by introducing a DNA sequence of (dT)14 next to the first start codon of pRSET. The effectiveness of frame-insensitive cloning was validated by inserting the gene encoding eGFP with all three possible frames to the vector. After transformation with one of these plasmids, E. coli cells expressed eGFP with no significant difference in the expression level. The pRSET-TriEX vector was then used for expression cloning of a novel fluorescent protein from Scolionema suvaense. We screened 3658 E. coli colonies transformed with pRSET-TriEX containing Scolionema suvaense cDNA, and found one colony expressing a novel green fluorescent protein, ScSuFP. The highest score in protein sequence similarity was 42% with the chain c of multi-domain green fluorescent protein like protein "ember" from Anthoathecata sp. Variations in the N- and/or C-terminal sequence of ScSuFP compared to other fluorescent proteins indicate that the expression cloning, rather than the sequence similarity-based methods, was crucial for acquiring the gene encoding ScSuFP. The absorption maximum was at 498 nm, with an extinction efficiency of 1.17 × 10⁵ M-1·cm-1. The emission maximum was at 511 nm and the fluorescence quantum yield was determined to be 0.6. Pseudo-native gel electrophoresis showed that the protein forms obligatory homodimers.
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Affiliation(s)
- Yuki Horiuchi
- Department of Bioengineering, Graduate School of Science and Engineering, Yamagata University, 992-8510 Yonezawa, Japan.
| | - Danai Laskaratou
- Biomolecular Network Dynamics, Biochemistry, Molecular and Structural Biology Section, KU Leuven, Celestijnenlaan 200g Box 2403, 3001 Leuven, Belgium.
| | - Michel Sliwa
- Laboratoire de Spectrochimie Infrarouge et Raman, Université de Lille, CNRS, UMR 8516, LASIR, F59 000 Lille, France.
| | - Cyril Ruckebusch
- Laboratoire de Spectrochimie Infrarouge et Raman, Université de Lille, CNRS, UMR 8516, LASIR, F59 000 Lille, France.
| | - Kuniyuki Hatori
- Department of Bio-System Engineering, Graduate School of Science and Engineering, Yamagata University, 992-8510 Yonezawa, Japan.
| | - Hideaki Mizuno
- Biomolecular Network Dynamics, Biochemistry, Molecular and Structural Biology Section, KU Leuven, Celestijnenlaan 200g Box 2403, 3001 Leuven, Belgium.
| | - Jun-Ichi Hotta
- Department of Bio-System Engineering, Graduate School of Science and Engineering, Yamagata University, 992-8510 Yonezawa, Japan.
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Lin AH, Liu Y, Burrascano C, Cunanan K, Logg CR, Robbins JM, Kasahara N, Gruber H, Ibañez C, Jolly DJ. Extensive Replication of a Retroviral Replicating Vector Can Expand the A Bulge in the Encephalomyocarditis Virus Internal Ribosome Entry Site and Change Translation Efficiency of the Downstream Transgene. Hum Gene Ther Methods 2016; 27:59-70. [PMID: 26918465 DOI: 10.1089/hgtb.2015.131] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
We have developed retroviral replicating vectors (RRV) derived from Moloney murine gammaretrovirus with an amphotropic envelope and an encephalomyocarditis virus (EMCV) internal ribosome entry site (IRES)-transgene cassette downstream of the env gene. During long-term (180 days) replication of the vector in animals, a bulge of 7 adenosine residues (A's) in the J-K bifurcation domain sometimes serially added A's. Therefore, vectors with 4-12 A's in the A bulge in the J-K bifurcation domain were generated, and the impact of the variants on transgene protein expression, vector stability, and IRES sequence upon multiple infection cycles was assessed in RRV encoding yeast-derived cytosine deaminase and green fluorescent protein in vitro. For transgene protein expression, after multiple infection cycles, RRV-IRES with 5-7 A's gave roughly comparable levels, 4 and 8 A's were within about 4-5-fold of the 6 A's, whereas 10 and 12 A's were marked lower. In terms of stability, after 10 infection cycles, expansion of A's appeared to be a more frequent event affecting transgene protein expression than viral genome deletions or rearrangement: 4 and 5 A's appeared completely stable; 6, 7, and particularly 8 A's showed some level of expansion in the A bulge; 10 and 12 A's underwent both expansion and transgene deletion. The strong relative translational activity of the 5 A's in the EMCV IRES has not been reported previously. The 5A RRV-IRES may have utility for preclinical and clinical applications where extended replication is required.
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Affiliation(s)
- Amy H Lin
- 1 Tocagen Inc. , San Diego, California
| | | | | | | | - Christopher R Logg
- 2 Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California-Los Angeles , Los Angeles, California
| | | | - Noriyuki Kasahara
- 2 Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California-Los Angeles , Los Angeles, California.,3 Department of Cell Biology, Miller School of Medicine, University of Miami , Miami, Florida
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Grebneva HA. Mechanisms of targeted frameshift mutations: Insertions arising during error-prone or SOS synthesis of DNA containing cis-syn cyclobutane thymine dimers. Mol Biol 2014. [DOI: 10.1134/s0026893314030066] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Arana ME, Seki M, Wood RD, Rogozin IB, Kunkel TA. Low-fidelity DNA synthesis by human DNA polymerase theta. Nucleic Acids Res 2008; 36:3847-56. [PMID: 18503084 PMCID: PMC2441791 DOI: 10.1093/nar/gkn310] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2008] [Revised: 04/28/2008] [Accepted: 04/30/2008] [Indexed: 12/14/2022] Open
Abstract
Human DNA polymerase theta (pol or POLQ) is a proofreading-deficient family A enzyme implicated in translesion synthesis (TLS) and perhaps in somatic hypermutation (SHM) of immunoglobulin genes. These proposed functions and kinetic studies imply that pol may synthesize DNA with low fidelity. Here, we show that when copying undamaged DNA, pol generates single base errors at rates 10- to more than 100-fold higher than for other family A members. Pol adds single nucleotides to homopolymeric runs at particularly high rates, exceeding 1% in certain sequence contexts, and generates single base substitutions at an average rate of 2.4 x 10(-3), comparable to inaccurate family Y human pol kappa (5.8 x 10(-3)) also implicated in TLS. Like pol kappa, pol is processive, implying that it may be tightly regulated to avoid deleterious mutagenesis. Pol also generates certain base substitutions at high rates within sequence contexts similar to those inferred to be copied by pol during SHM of immunoglobulin genes in mice. Thus, pol is an exception among family A polymerases, and its low fidelity is consistent with its proposed roles in TLS and SHM.
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Affiliation(s)
- Mercedes E. Arana
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, NIEHS, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, Department of Pharmacology, University of Pittsburgh Medical School, Hillman Cancer Center, Research Pavilion Suite 2.6, 5117 Centre Avenue, Pittsburgh, PA 15213-1863 and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20894, USA
| | - Mineaki Seki
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, NIEHS, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, Department of Pharmacology, University of Pittsburgh Medical School, Hillman Cancer Center, Research Pavilion Suite 2.6, 5117 Centre Avenue, Pittsburgh, PA 15213-1863 and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20894, USA
| | - Richard D. Wood
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, NIEHS, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, Department of Pharmacology, University of Pittsburgh Medical School, Hillman Cancer Center, Research Pavilion Suite 2.6, 5117 Centre Avenue, Pittsburgh, PA 15213-1863 and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20894, USA
| | - Igor B. Rogozin
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, NIEHS, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, Department of Pharmacology, University of Pittsburgh Medical School, Hillman Cancer Center, Research Pavilion Suite 2.6, 5117 Centre Avenue, Pittsburgh, PA 15213-1863 and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20894, USA
| | - Thomas A. Kunkel
- Laboratory of Molecular Genetics and Laboratory of Structural Biology, NIEHS, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, Department of Pharmacology, University of Pittsburgh Medical School, Hillman Cancer Center, Research Pavilion Suite 2.6, 5117 Centre Avenue, Pittsburgh, PA 15213-1863 and National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Department of Health and Human Services, Bethesda, MD 20894, USA
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Minoda A, Sakagami R, Yagisawa F, Kuroiwa T, Tanaka K. Improvement of Culture Conditions and Evidence for Nuclear Transformation by Homologous Recombination in a Red Alga, Cyanidioschyzon merolae 10D. ACTA ACUST UNITED AC 2004; 45:667-71. [PMID: 15215501 DOI: 10.1093/pcp/pch087] [Citation(s) in RCA: 133] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Although the nuclear genome sequence of Cyanidioschyzon merolae 10D, a unicellular red alga, was recently determined, DNA transformation technology that is important as a model plant system has never been available thus far. In this study, improved culture conditions resulted in a faster growth rate of C. merolae in liquid medium (doubling time = 9.2 h), and colony formation on gellan gum plates. Using these conditions, spontaneous mutants (5-fluoroortic acid resistant) deficient in the UMP synthase gene were isolated. The lesions were then restored by introducing the wild-type UMP synthase gene into the cells suggesting DNA transformation by homologous recombination.
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Affiliation(s)
- Ayumi Minoda
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, 113-0032 Japan
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Pavlov YI, Maki S, Maki H, Kunkel TA. Evidence for interplay among yeast replicative DNA polymerases alpha, delta and epsilon from studies of exonuclease and polymerase active site mutations. BMC Biol 2004; 2:11. [PMID: 15163346 PMCID: PMC434536 DOI: 10.1186/1741-7007-2-11] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2004] [Accepted: 05/26/2004] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA polymerase epsilon (Pol epsilon) is essential for S-phase replication, DNA damage repair and checkpoint control in yeast. A pol2-Y831A mutation leading to a tyrosine to alanine change in the Pol epsilon active site does not cause growth defects and confers a mutator phenotype that is normally subtle but strong in a mismatch repair-deficient strain. Here we investigate the mechanism responsible for the mutator effect. RESULTS Purified four-subunit Y831A Pol epsilon turns over more deoxynucleoside triphosphates to deoxynucleoside monophosphates than does wild-type Pol epsilon, suggesting altered coordination between the polymerase and exonuclease active sites. The pol2-Y831A mutation suppresses the mutator effect of the pol2-4 mutation in the exonuclease active site that abolishes proofreading by Pol epsilon, as measured in haploid strain with the pol2-Y831A,4 double mutation. Analysis of mutation rates in diploid strains reveals that the pol2-Y831A allele is recessive to pol2-4. In addition, the mutation rates of strains with the pol2-4 mutation in combination with active site mutator mutations in Pol delta and Pol alpha suggest that Pol epsilon may proofread certain errors made by Pol alpha and Pol delta during replication in vivo. CONCLUSIONS Our data suggest that Y831A replacement in Pol epsilon reduces replication fidelity and its participation in chromosomal replication, but without eliminating an additional function that is essential for viability. This suggests that other polymerases can substitute for certain functions of polymerase epsilon.
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Affiliation(s)
- Youri I Pavlov
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institute of Health, DHHS, Research Triangle Park, NC 27709, USA
- Eppley Institute for Research in Cancer and Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Satoko Maki
- Laboratory of Microbial Molecular Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara 630-01, Japan
| | - Hisaji Maki
- Laboratory of Microbial Molecular Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Nara 630-01, Japan
| | - Thomas A Kunkel
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institute of Health, DHHS, Research Triangle Park, NC 27709, USA
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences National Institute of Health, DHHS, Research Triangle Park, NC 27709, USA
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Maki H. Origins of spontaneous mutations: specificity and directionality of base-substitution, frameshift, and sequence-substitution mutageneses. Annu Rev Genet 2003; 36:279-303. [PMID: 12429694 DOI: 10.1146/annurev.genet.36.042602.094806] [Citation(s) in RCA: 106] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Spontaneous mutations are derived from various sources, including errors made during replication of undamaged template DNA, mutagenic nucleotide substrates, and endogenous DNA lesions. These sources vary in their frequencies and resultant mutations, and are differently affected by the DNA sequence, DNA transactions, and cellular metabolism. Organisms possess a variety of cellular functions to suppress spontaneous mutagenesis, and the specificity and effectiveness of each function strongly affect the pattern of spontaneous mutations. Base substitutions and single-base frameshifts, two major classes of spontaneous mutations, occur non-randomly throughout the genome. Within target DNA sequences there are hotspots for particular types of spontaneous mutations; outside of the hotspots, spontaneous mutations occur more randomly and much less frequently. Hotspot mutations are attributable more to endogenous DNA lesions than to replication errors. Recently, a novel class of mutagenic pathway that depends on short inverted repeats was identified as another important source of hotspot mutagenesis.
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Affiliation(s)
- Hisaji Maki
- Department of Molecular Biology, Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan.
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Viguera E, Canceill D, Ehrlich SD. Replication slippage involves DNA polymerase pausing and dissociation. EMBO J 2001; 20:2587-95. [PMID: 11350948 PMCID: PMC125466 DOI: 10.1093/emboj/20.10.2587] [Citation(s) in RCA: 199] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Genome rearrangements can take place by a process known as replication slippage or copy-choice recombination. The slippage occurs between repeated sequences in both prokaryotes and eukaryotes, and is invoked to explain microsatellite instability, which is related to several human diseases. We analysed the molecular mechanism of slippage between short direct repeats, using in vitro replication of a single-stranded DNA template that mimics the lagging strand synthesis. We show that slippage involves DNA polymerase pausing, which must take place within the direct repeat, and that the pausing polymerase dissociates from the DNA. We also present evidence that, upon polymerase dissociation, only the terminal portion of the newly synthesized strand separates from the template and anneals to another direct repeat. Resumption of DNA replication then completes the slippage process.
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Affiliation(s)
- E Viguera
- Laboratoire de Génétique Microbienne, Institut National de la Recherche Agronomique, Domaine de Vilvert, 78350 Jouy en Josas, France.
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Organization, Replication, Transposition, and Repair of DNA. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50030-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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