Burnouf D. Y., Olieric V., Wagner J., Fujii S., Reinbolt J., Fuchs R. P., Dumas P.
Structural and biochemical analysis of sliding clamp/ligand interactions suggest a competition between replicative and translesion DNA polymerases Article de journal
Dans: J Mol Biol, vol. 335, no. 5, p. 1187-97, 2004, (0022-2836 Journal Article).
Résumé | BibTeX | Étiquettes: *Binding, Antigen/metabolism, Bacterial/genetics, beta/*chemistry/genetics/*metabolism, Binding, Cell, coli/*enzymology, Competitive, Crystallization, DNA, DUMAS, Escherichia, Fragments/*metabolism, I/metabolism, III/metabolism, Kinetics, ligands, Models, Molecular, Nuclear, Peptide, Polymerase, Proliferating, Protein, Proteins/chemistry/metabolism, Recombinant, Replication/*genetics, Subunits
@article{,
title = {Structural and biochemical analysis of sliding clamp/ligand interactions suggest a competition between replicative and translesion DNA polymerases},
author = { D. Y. Burnouf and V. Olieric and J. Wagner and S. Fujii and J. Reinbolt and R. P. Fuchs and P. Dumas},
year = {2004},
date = {2004-01-01},
journal = {J Mol Biol},
volume = {335},
number = {5},
pages = {1187-97},
abstract = {Most DNA polymerases interact with their cognate processive replication factor through a small peptide, this interaction being absolutely required for their function in vivo. We have solved the crystal structure of a complex between the beta sliding clamp of Escherichia coli and the 16 residue C-terminal peptide of Pol IV (P16). The seven C-terminal residues bind to a pocket located at the surface of one beta monomer. This region was previously identified as the binding site of another beta clamp binding protein, the delta subunit of the gamma complex. We show that peptide P16 competitively prevents beta-clamp-mediated stimulation of both Pol IV and alpha subunit DNA polymerase activities, suggesting that the site of interaction of the alpha subunit with beta is identical with, or overlaps that of Pol IV. This common binding site for delta, Pol IV and alpha subunit is shown to be formed by residues that are highly conserved among many bacterial beta homologs, thus defining an evolutionarily conserved hydrophobic crevice for sliding clamp ligands and a new target for antibiotic drug design.},
note = {0022-2836
Journal Article},
keywords = {*Binding, Antigen/metabolism, Bacterial/genetics, beta/*chemistry/genetics/*metabolism, Binding, Cell, coli/*enzymology, Competitive, Crystallization, DNA, DUMAS, Escherichia, Fragments/*metabolism, I/metabolism, III/metabolism, Kinetics, ligands, Models, Molecular, Nuclear, Peptide, Polymerase, Proliferating, Protein, Proteins/chemistry/metabolism, Recombinant, Replication/*genetics, Subunits},
pubstate = {published},
tppubtype = {article}
}
Mohr S., Bottin M. C., Lannes B., Neuville A., Bellocq J. P., Keith G., Rihn B. H.
Microdissection, mRNA amplification and microarray: a study of pleural mesothelial and malignant mesothelioma cells Article de journal
Dans: Biochimie, vol. 86, no. 1, p. 13-9, 2004, (0300-9084 Journal Article).
Résumé | BibTeX | Étiquettes: Analysis, Array, Chain, Epithelium/*metabolism, Expression, Female, Gene, Genetic, Human, KEITH, Lasers, Male, Markers, Mesothelioma/*genetics/metabolism, messenger, Microdissection, Neoplasms/*genetics/metabolism, Neoplastic/*genetics, Oligonucleotide, Pleura/*cytology/*metabolism, Pleural, Polymerase, Profiling, Reaction, Regulation, Reverse, RNA, Sequence, Transcriptase
@article{,
title = {Microdissection, mRNA amplification and microarray: a study of pleural mesothelial and malignant mesothelioma cells},
author = { S. Mohr and M.C. Bottin and B. Lannes and A. Neuville and J.P. Bellocq and G. Keith and B.H. Rihn},
year = {2004},
date = {2004-01-01},
journal = {Biochimie},
volume = {86},
number = {1},
pages = {13-9},
abstract = {The studies of molecular alterations in tumor cells with microarrays are often hampered by inherent tissue heterogeneity. The emergence of Laser Capture Microdissection (LCM) allowed us to overcome this challenge since it gives selective access to cancer cells that are isolated from their native tissue environment. In this report, we microdissected mesothelial cells and malignant mesothelioma cells of ex vivo resected specimens using LCM. Amplified RNA from mesothelial and mesothelioma microdissected cells allowed us to measure global gene expression with 10 K-microarrays in four independent experiments. We screened 9850 annotated human genes, 1275 of which have satisfied our data analysis requirements. They included 302 overexpressed genes and 160 downregulated genes in mesothelioma microdissected cells as compared to mesothelial microdissected cells. Among them, the expression levels of eight genes, namely BF, FTL, IGFBP7, RARRES1, RARRES2, RBP1, SAT, and TXN according to HUGO nomenclature, were increased, whereas six: ALOX5AP, CLNS1A, EIF4A2, ELK3, REQ and SYPL, were found to be underexpressed in mesothelioma microdissected cells. The ferritin light polypeptide (FTL) gene overexpression was confirmed by real time quantitative PCR. Our approach allowed a comprehensive in situ examination of mesothelioma and provided an accurate way to find new marker genes that may be useful for diagnosis and treatment of malignant pleural mesothelioma.},
note = {0300-9084
Journal Article},
keywords = {Analysis, Array, Chain, Epithelium/*metabolism, Expression, Female, Gene, Genetic, Human, KEITH, Lasers, Male, Markers, Mesothelioma/*genetics/metabolism, messenger, Microdissection, Neoplasms/*genetics/metabolism, Neoplastic/*genetics, Oligonucleotide, Pleura/*cytology/*metabolism, Pleural, Polymerase, Profiling, Reaction, Regulation, Reverse, RNA, Sequence, Transcriptase},
pubstate = {published},
tppubtype = {article}
}
Rihn B. H., Mohr S., McDowell S. A., Binet S., Loubinoux J., Galateau F., Keith G., Leikauf G. D.
Differential gene expression in mesothelioma Article de journal
Dans: FEBS Lett, vol. 480, no. 2-3, p. 95-100, 2000, (0014-5793 Journal Article).
Résumé | BibTeX | Étiquettes: *Gene, Adhesion, Analysis/methods, Array, Cell, Cells, Chain, Cultured, Cycle, Division, Expression, Gene, Human, Invasiveness, Mesothelioma/*genetics/metabolism, Neoplasm, Neoplastic, Oligonucleotide, Oxidative, Polymerase, Profiling, Proteins/metabolism, Reaction, Regulation, Reverse, Sequence, Stress, Transcriptase, tumor, Xenobiotics
@article{,
title = {Differential gene expression in mesothelioma},
author = { B. H. Rihn and S. Mohr and S. A. McDowell and S. Binet and J. Loubinoux and F. Galateau and G. Keith and G. D. Leikauf},
year = {2000},
date = {2000-01-01},
journal = {FEBS Lett},
volume = {480},
number = {2-3},
pages = {95-100},
abstract = {To investigate the molecular events controlling malignant transformation of human pleural cells, we compared constitutive gene expression of mesothelioma cells to that of pleural cells. Using cDNA microarray and high-density filter array, we assessed expression levels of > 6500 genes. Most of the highly expressed transcripts were common to both cell lines and included genes associated with stress response and DNA repair, outcomes consistent with the radio- and chemo-resistance of mesothelioma. Interestingly, of the fewer than 300 genes that differed between cell lines, most functioned in (i) macromolecule stability, (ii) cell adhesion and recognition, (iii) cell migration (invasiveness), and (iv) extended cell division. Expression levels of several of these genes were confirmed by RT-PCR and could be useful as diagnostic markers of human mesothelioma.},
note = {0014-5793
Journal Article},
keywords = {*Gene, Adhesion, Analysis/methods, Array, Cell, Cells, Chain, Cultured, Cycle, Division, Expression, Gene, Human, Invasiveness, Mesothelioma/*genetics/metabolism, Neoplasm, Neoplastic, Oligonucleotide, Oxidative, Polymerase, Profiling, Proteins/metabolism, Reaction, Regulation, Reverse, Sequence, Stress, Transcriptase, tumor, Xenobiotics},
pubstate = {published},
tppubtype = {article}
}
Wilhelm M., Heyman T., Friant S., Wilhelm F. X.
Heterogeneous terminal structure of Ty1 and Ty3 reverse transcripts Article de journal
Dans: Nucleic Acids Res, vol. 25, no. 11, p. 2161-6, 1997, (0305-1048 Journal Article).
Résumé | BibTeX | Étiquettes: *Nucleic, *Transcription, Acid, Calf, Chain, Conformation, DNA, Fungal/*chemistry/metabolism, Genetic, Gov't, H, Hybridization, Non-U.S., Nucleic, Plasmids/chemistry/genetics/metabolism, Polymerase, Reaction, Replication, Retroelements/*genetics, Ribonuclease, RNA, Support, Thymus/metabolism, Transfer/chemistry
@article{,
title = {Heterogeneous terminal structure of Ty1 and Ty3 reverse transcripts},
author = { M. Wilhelm and T. Heyman and S. Friant and F. X. Wilhelm},
year = {1997},
date = {1997-01-01},
journal = {Nucleic Acids Res},
volume = {25},
number = {11},
pages = {2161-6},
abstract = {A specific terminal structure of preintegrative DNA is required for transposition of retroviruses and LTR-retrotransposons. We have used an anchored PCR technique to map the 3'ends of DNA intermediates synthesized inside yeast Ty1 and Ty3 retrotransposon virus-like particles. We find that, unlike retroviruses, Ty1 replicated DNA does not have two extra base pairs at its 3'ends. In contrast some Ty3 preintegrative DNA molecules have two extra nucleotides at the 3'end of upstream and downstream long terminal repeats. Moreover we find that some molecules of replicated Ty3 DNA have more than two extra nucleotides at the 3'end of the upstream LTR. This observation could be accounted for by imprecise RNAse H cutting of the PPT sequence. The site of Ty1 and Ty3 plus-strand strong-stop DNA termination was also examined. Our results confirm that the prominent Ty1 and Ty3 plus-strand strong-stop molecules harbor 12 tRNA templated bases but also show that some Ty1 and Ty3 plus-strand strong-stop DNA molecules harbor less tRNA templated bases. We propose that these less than full length plus-strand molecules could be active intermediates in Ty retrotransposon replication.},
note = {0305-1048
Journal Article},
keywords = {*Nucleic, *Transcription, Acid, Calf, Chain, Conformation, DNA, Fungal/*chemistry/metabolism, Genetic, Gov't, H, Hybridization, Non-U.S., Nucleic, Plasmids/chemistry/genetics/metabolism, Polymerase, Reaction, Replication, Retroelements/*genetics, Ribonuclease, RNA, Support, Thymus/metabolism, Transfer/chemistry},
pubstate = {published},
tppubtype = {article}
}
Heyman T., Agoutin B., Friant S., Wilhelm F. X., Wilhelm M. L.
Plus-strand DNA synthesis of the yeast retrotransposon Ty1 is initiated at two sites, PPT1 next to the 3' LTR and PPT2 within the pol gene. PPT1 is sufficient for Ty1 transposition Article de journal
Dans: J Mol Biol, vol. 253, no. 2, p. 291-303, 1995, (0022-2836 Journal Article).
Résumé | BibTeX | Étiquettes: *DNA, *Genes, *Repetitive, *Retroelements, Acid, Base, C/analysis, cerevisiae/genetics/*virology, Chain, Cloning, Data, DNA, Fungal, Fungal/biosynthesis, Genes, Genetic, Genome, Gov't, Mapping, Molecular, Non-U.S., Nucleic, pol, Poly, Polymerase, Primers, Reaction, Replication, Restriction, Saccharomyces, Sequence, Sequences, Support, Transcription, Viral, Viral/*biosynthesis
@article{,
title = {Plus-strand DNA synthesis of the yeast retrotransposon Ty1 is initiated at two sites, PPT1 next to the 3' LTR and PPT2 within the pol gene. PPT1 is sufficient for Ty1 transposition},
author = { T. Heyman and B. Agoutin and S. Friant and F. X. Wilhelm and M. L. Wilhelm},
year = {1995},
date = {1995-01-01},
journal = {J Mol Biol},
volume = {253},
number = {2},
pages = {291-303},
abstract = {Long terminal repeat elements and retroviruses require primers for initiation of minus and plus-strand DNA synthesis by reverse transcriptase. Here we demonstrate genetically that plus-strand DNA synthesis of the yeast Ty1 element is initiated at two sites located at the 5' boundary of the 3' long terminal repeat (PPT1) and near the middle of the pol gene in the integrase coding sequence (PPT2). A consequence of the presence of two PPTs is that Ty1 plus-strand DNA exists as segments at some time during replication. Three fragments have been identified: the plus-strand strong-stop DNA initiated at PPT1, a downstream fragment initiated at PPT2 and an upstream fragment spanning the 5'-terminal part of Ty1 and a portion of the TyB gene. Characterization of the 3' ends of the plus-strand DNA fragments reveals (1) that the upstream fragment is elongated beyond PPT2 creating a plus-strand overlap and (2) that the majority of plus-strand strong-stop DNA fragments bear a copy of the minus-strand primer binding site in agreement with the accepted model of retroviral genomic RNA reverse transcription. The two polypurine tracts, PPT1 and PPT2, have an identical sequence GGGTGGTA. Mutations replacing purines by pyrimidines in this sequence significantly diminish or abolish initiation of plus-strand synthesis. Ty1 elements bearing a mutated PPT2 sequence are not defective for transposition whereas mutations in PPT1 abolish transposition.},
note = {0022-2836
Journal Article},
keywords = {*DNA, *Genes, *Repetitive, *Retroelements, Acid, Base, C/analysis, cerevisiae/genetics/*virology, Chain, Cloning, Data, DNA, Fungal, Fungal/biosynthesis, Genes, Genetic, Genome, Gov't, Mapping, Molecular, Non-U.S., Nucleic, pol, Poly, Polymerase, Primers, Reaction, Replication, Restriction, Saccharomyces, Sequence, Sequences, Support, Transcription, Viral, Viral/*biosynthesis},
pubstate = {published},
tppubtype = {article}
}