Biologie Digitale de l’ARN

@article{hammann_method_2014,

title = {A method to map changes in bacterial surface composition induced by regulatory RNAs in Escherichia coli and Staphylococcus aureus.},

author = {P Hammann and D Parmentier and M Cerciat and J Reimegård and A-C Helfer and S Boisset and M Guillier and F Vandenesch and G E H Wagner and P Romby and P Fechter},

doi = {10.1016/j.biochi.2014.07.011},

issn = {1638-6183 0300-9084},

year  = {2014},

date = {2014-01-01},

journal = {Biochimie},

volume = {106},

pages = {175--179},

abstract = {We have adapted a method to map cell surface proteins and to monitor the effect of specific regulatory RNAs on the surface composition of the bacteria. This method involves direct labeling of surface proteins of living bacteria using fluorescent dyes and a subsequent separation of the crude extract by 2D gel electrophoresis. The strategy yields a substantial enrichment in surface proteins over cytoplasmic proteins. We validated this method by monitoring the effect of the regulatory RNA MicA in Escherichia coli, which regulates the synthesis of several outer membrane proteins, and highlighted the role of Staphylococcus aureus RNAIII for the maintenance of cell wall integrity.},

note = {Place: France},

keywords = {Bacterial Outer Membrane Proteins/metabolism, Bacterial Proteins/*metabolism, Bacterial/genetics/*metabolism, Base Sequence, Carbocyanines/metabolism, Cell Membrane/*metabolism, Cell Wall/metabolism, Confocal, DIGE, Electrophoresis, Escherichia coli/genetics/*metabolism, Gel, Mass, Matrix-Assisted Laser Desorption-Ionization, Microscopy, Molecular Sequence Data, Non-coding RNAs, Post-transcriptional regulation, PPSE, Reproducibility of Results, RNA, Spectrometry, Staining and Labeling/methods, Staphylococcus aureus/genetics/*metabolism, Surface proteins, Two-Dimensional/methods},

pubstate = {published},

tppubtype = {article}

}

@article{hamrita_proteomics-based_2009,

title = {Proteomics-based identification of alpha1-antitrypsin and haptoglobin precursors as novel serum markers in infiltrating ductal breast carcinomas.},

author = {Bechr Hamrita and Karim Chahed and Mounir Trimeche and Christelle Lemaitre Guillier and Philippe Hammann and Anouar Chaïeb and Sadok Korbi and Lotfi Chouchane},

doi = {10.1016/j.cca.2009.03.033},

issn = {1873-3492 0009-8981},

year  = {2009},

date = {2009-06-01},

journal = {Clinica chimica acta; international journal of clinical chemistry},

volume = {404},

number = {2},

pages = {111--118},

abstract = {BACKGROUND: The identification of pathological markers of breast cancer for either diagnosis, treatment response or for survival is of critical importance. METHODS: Serum protein profiling using 2-DE separations coupled to matrix-assisted laser desorption ionization mass spectrometry has been used to explore protein alterations in patients with infiltrating ductal breast carcinomas (IDCA). Sera from 39 breast cancer patients and 40 healthy controls were selected for screening study using 2-DE combined with MS. The protein expression patterns obtained after the depletion of high abundance proteins was determined by coomassie blue G-250 stain after 2-DE electrophoresis. RESULTS: Six proteins that expressed differentially in the IDCA group were found. The expression levels of four isoforms corresponding to haptoglobin precursor and two isoforms of alpha1-antitrypsin precursor (alpha1-AT) were upregulated in sera from breast cancer patients. There was an increased expression of both proteins in the sera of patients with various tumor stages (I, II, III) in comparison to healthy women. Applying immunohistochemistry, we further validated alpha1-AT immunoreactivity in 51 formalin-fixed paraffin-embedded sections of breast tumors. Enhanced expression of alpha1-AT like activity has been found in IDCA breast tumors, as well as, in different histological types of breast cancer. No significant association has been found with lymph node occurrence, while in high tumor categories a tendency to an increased expression of alpha1-AT has been found, thereby suggesting a possible role of this protein in tumor growth. CONCLUSIONS: These proteins may constitute new and useful markers of breast cancer that offer a clue to a better understanding of inflammatory pathways and carcinogenesis events linked to breast cancer progression.},

note = {Place: Netherlands},

keywords = {80 and over, Adult, Aged, alpha 1-Antitrypsin/*blood, Amino Acid Sequence, Biomarkers, Breast Neoplasms/blood/*pathology, Carcinoma, Ductal/blood/*pathology, Electrophoresis, Female, Gel, Haptoglobins/*analysis, Humans, Mass, Matrix-Assisted Laser Desorption-Ionization, Middle Aged, Molecular Sequence Data, PPSE, Protein Isoforms/blood, proteomics, Spectrometry, Tumor/*blood, Two-Dimensional},

pubstate = {published},

tppubtype = {article}

}

@article{wilkins_differences_2009,

title = {Differences in hydroxylation and binding of Notch and HIF-1alpha demonstrate substrate selectivity for factor inhibiting HIF-1 (FIH-1).},

author = {Sarah E Wilkins and Jaana Hyvärinen and Johana Chicher and Jeffrey J Gorman and Daniel J Peet and Rebecca L Bilton and Peppi Koivunen},

doi = {10.1016/j.biocel.2009.01.005},

issn = {1878-5875 1357-2725},

year  = {2009},

date = {2009-01-01},

journal = {The international journal of biochemistry & cell biology},

volume = {41},

number = {7},

pages = {1563--1571},

abstract = {FIH-1, factor inhibiting hypoxia-inducible factor-1 (HIF-1), regulates oxygen sensing by hydroxylating an asparagine within HIF-alpha. It also hydroxylates asparagines in many proteins containing ankyrin repeats, including Notch1-3, p105 and I?B?. Relative binding affinity and hydroxylation rate are crucial determinants of substrate selection and modification. We determined the contributions of substrate sequence composition and length and of oxygen concentration to the FIH-1-binding and/or hydroxylation of Notch1-4 and compared them with those for HIF-1alpha. We also demonstrated hydroxylation of two asparagines in Notch2 and 3, corresponding to Sites 1 and 2 of Notch1, by mass spectrometry for the first time. Our data demonstrate that substrate length has a much greater influence on FIH-1-dependent hydroxylation of Notch than of HIF-1alpha, predominantly through binding affinity rather than maximal reaction velocity. The K(m) value of FIH-1 for Notch1, textless 0.2 microM, is at least 250-fold lower than that of 50 microM for HIF-1alpha. Site 1 of Notch1-3 appeared the preferred site of FIH-1 hydroxylation in these substrates. Interestingly, binding of Notch4 to FIH-1 was observed with an affinity almost 10-fold lower than for Notch1-3, but no hydroxylation was detected. Importantly, we demonstrate that the K(m) of FIH-1 for oxygen at the preferred Site 1 of Notch1-3, 10-19 microM, is an order of magnitude lower than that for Site 2 or HIF-1alpha. Hence, at least during in vitro hydroxylation, Notch is likely to become efficiently hydroxylated by FIH-1 even under relatively severe hypoxic conditions, where HIF-1alpha hydroxylation would be reduced.},

note = {Place: Netherlands},

keywords = {alpha Subunit/*metabolism, Amino Acid Sequence, Animals, Asparagine/metabolism, Humans, Hydroxylation, Hypoxia-Inducible Factor 1, Kinetics, Mice, Mixed Function Oxygenases, Molecular Sequence Data, Notch/chemistry/*metabolism, Oxygen/metabolism, Peptides/chemistry/metabolism, PPSE, Protein Binding, Receptors, Recombinant Proteins/metabolism, Repressor Proteins/*metabolism, Substrate Specificity},

pubstate = {published},

tppubtype = {article}

}

@article{geotti-bianchini_design_2008,

title = {Design and synthesis of intrinsically cell-penetrating nucleopeptides},

author = {Piero Geotti-Bianchini and Julien Beyrath and Olivier Chaloin and Fernando Formaggio and Alberto Bianco},

doi = {10.1039/b811639c},

issn = {1477-0539},

year  = {2008},

date = {2008-10-01},

journal = {Organic & Biomolecular Chemistry},

volume = {6},

number = {20},

pages = {3661--3663},

abstract = {Nucleopeptides, which are constituted of alpha-amino acids bearing nucleobases at their side chains, are able to penetrate into cells and to reach the nucleus without cytotoxic effects.},

keywords = {Amino Acid Sequence, Cell Line, Cells, Drug Design, Humans, I2CT, Molecular Sequence Data, Peptides, Purines, Pyrimidines, Team-Bianco},

pubstate = {published},

tppubtype = {article}

}

@article{monneaux_importance_2007,

title = {Importance of spliceosomal RNP1 motif for intermolecular Ŧ-B cell spreading and tolerance restoration in lupus},

author = {Fanny Monneaux and Véronique Parietti and Jean-Paul Briand and Sylviane Muller},

doi = {10.1186/ar2317},

issn = {1478-6362},

year  = {2007},

date = {2007-01-01},

journal = {Arthritis Research & Therapy},

volume = {9},

number = {5},

pages = {R111},

abstract = {We previously demonstrated the importance of the RNP1 motif-bearing region 131-151 of the U1-70K spliceosomal protein in the intramolecular T-B spreading that occurs in MRL/lpr lupus mice. Here, we analyze the involvement of RNP1 motif in the development and prevention of naturally-occurring intermolecular T-B cell diversification. We found that MRL/lpr peripheral blood lymphocytes proliferated in response to peptides containing or corresponding exactly to the RNP1 motif of spliceosomal U1-70K, U1-A and hnRNP-A2 proteins. We also demonstrated that rabbit antibodies to peptide 131-151 cross-reacted with U1-70K, U1-A and hnRNP-A2 RNP1-peptides. These antibodies recognized the U1-70K and U1-A proteins, and also U1-C and SmD1 proteins, which are devoid of RNP1 motif. Repeated administration of phosphorylated peptide P140 into MRL/lpr mice abolished T-cell response to several peptides from the U1-70K, U1-A and SmD1 proteins without affecting antibody and T-cell responses to foreign (viral) antigen in treated mice challenged with infectious virus. These results emphasized the importance of the dominant RNP1 region, which seems to be central in the activation cascade of B and T cells reacting with spliceosomal RNP1+ and RNP1- spliceosomal proteins. The tolerogenic peptide P140, which is recognized by lupus patients' CD4+ T cells and known to protect MRL/lpr mice, is able to thwart emergence of intermolecular T-cell spreading in treated animals.},

keywords = {Amino Acid Motifs, Amino Acid Sequence, Animals, B-Lymphocytes, I2CT, Immune Tolerance, Inbred MRL lpr, Lupus Erythematosus, Mice, Molecular Sequence Data, Monneaux, Ribonucleoproteins, RNA-Binding Proteins, Saccharomyces cerevisiae Proteins, Spliceosomes, Systemic, T-Lymphocytes, Team-Dumortier},

pubstate = {published},

tppubtype = {article}

}

@article{monneaux_selective_2005,

title = {Selective modulation of CD4+ Ŧ cells from lupus patients by a promiscuous, protective peptide analog},

author = {Fanny Monneaux and Johan Hoebeke and Christelle Sordet and Céline Nonn and Jean-Paul Briand and Bernard Maillère and Jean Sibilia and Sylviane Muller},

doi = {10.4049/jimmunol.175.9.5839},

issn = {0022-1767},

year  = {2005},

date = {2005-11-01},

journal = {Journal of Immunology (Baltimore, Md.: 1950)},

volume = {175},

number = {9},

pages = {5839--5847},

abstract = {A peptide encompassing residues 131-151 of the spliceosomal U1-70K protein and its analog phosphorylated at Ser140 were synthesized as potential candidates for the treatment of patients with lupus. Studies in the MRL/lpr and (NZB x NZW)F1 lupus models have demonstrated that these sequences contain a CD4+ T cell epitope but administration of the phosphorylated peptide only ameliorates the clinical manifestations of treated MRL/lpr mice. Binding assays with soluble HLA class II molecules and molecular modeling experiments indicate that both peptides behave as promiscuous epitopes and bind to a large panel of human DR molecules. In contrast to normal T cells and T cells from non-lupus autoimmune patients, we found that PBMCs from 40% of lupus patients selected randomly and CFSE-labeled CD4+ T cells proliferate in response to peptide 131-151. Remarkably, however, we observed that phosphorylation of Ser140 prevents CD4+ T cells proliferation but not secretion of regulatory cytokines, suggesting a striking immunomodulatory effect of phosphorylated analog on lupus CD4+ T cells that was unique to patients. The analog might act as an activator of regulatory T cells or as a partial agonist of TCR.},

keywords = {Amino Acid Sequence, CD4-Positive T-Lymphocytes, HLA-DR Antigens, Humans, I2CT, Interleukin-10, Lupus Erythematosus, Lymphocyte Activation, Molecular Sequence Data, Monneaux, Peptide Fragments, Phosphorylation, Ribonucleoprotein, Systemic, Team-Dumortier, U1 Small Nuclear},

pubstate = {published},

tppubtype = {article}

}

@article{monneaux_t_2003,

title = {T cell recognition and therapeutic effect of a phosphorylated synthetic peptide of the 70K snRNP protein administered in MR/lpr mice},

author = {Fanny Monneaux and José Manuel Lozano and Manuel E Patarroyo and Jean-Paul Briand and Sylviane Muller},

doi = {10.1002/immu.200310002},

issn = {0014-2980},

year  = {2003},

date = {2003-01-01},

journal = {European Journal of Immunology},

volume = {33},

number = {2},

pages = {287--296},

abstract = {Modifications of self antigens that occur during apoptosis might be involved in the generation of neo-antigens, which can break tolerance and induce autoimmunity. We have previously identified an epitope at residues 131-151 of the U1-70K snRNP protein, recognized by IgG antibodies and CD4+ T cells from at least two strains of lupus mice. With the aim of investigating the possible role of phosphorylation on the antigenicity of peptide 131-151 and to gain a better understanding of how this peptide can drive autoimmune response, we synthesized two peptides phosphorylated on Ser137 and 140, respectively. We show here that peptide P140 phosphorylated on Ser140 is recognized by both CD4+ T cells and antibodies from MRL/lpr mice. Furthermore, intravenous administration to lupus-prone MRL/lpr mice of P140 in saline (but not of the non-phosphorylated peptide) decreased proteinuria and anti-DNA antibody production, and significantly prolonged survival of treated mice. We further demonstrated that P140 is recognized by antibodies from lupus patients and binds to various HLA DR molecules, offering new hope for manipulating T cell response in humans.},

keywords = {Amino Acid Sequence, Animal, Animals, Autoantibodies, Autoantigens, Autoimmune Diseases, B-Lymphocytes, Cross Reactions, Disease Models, Female, HLA-DR Antigens, HLA-DR Serological Subtypes, HLA-DR1 Antigen, HLA-DR4 Antigen, Humans, I2CT, Immunization, Immunotherapy, Inbred BALB C, Inbred MRL lpr, Lupus Erythematosus, Lupus Nephritis, Mice, Molecular Sequence Data, Monneaux, Peptide Fragments, Phosphorylation, Protein Binding, Ribonucleoprotein, Systemic, T-Lymphocytes, Team-Dumortier, U1 Small Nuclear},

pubstate = {published},

tppubtype = {article}

}

@article{monneaux_epitope_2002,

title = {Epitope spreading in systemic lupus erythematosus: identification of triggering peptide sequences},

author = {Fanny Monneaux and Sylviane Muller},

doi = {10.1002/art.10263},

issn = {0004-3591},

year  = {2002},

date = {2002-06-01},

journal = {Arthritis and Rheumatism},

volume = {46},

number = {6},

pages = {1430--1438},

keywords = {Amino Acid Sequence, Animals, B-Lymphocyte, Epitopes, Humans, I2CT, Lupus Erythematosus, Molecular Sequence Data, Monneaux, Systemic, T-Lymphocyte, Team-Dumortier},

pubstate = {published},

tppubtype = {article}

}

@article{bates_adamdec1_2002,

title = {The ADAMDEC1 (decysin) gene structure: evolution by duplication in a metalloprotease gene cluster on chromosome 8p12},

author = {Elizabeth E M Bates and Wolf H Fridman and Chris G F Mueller},

doi = {10.1007/s00251-002-0430-3},

issn = {0093-7711},

year  = {2002},

date = {2002-05-01},

journal = {Immunogenetics},

volume = {54},

number = {2},

pages = {96--105},

abstract = {Members of the ADAM superfamily of metalloprotease genes are involved in a number of biological processes, including fertilization, neurogenesis, muscle development, and the immune response. These proteins have been classified into several groups. The prototypic ADAM family is comprised of a pro-domain, a metalloprotease domain, a disintegrin domain, a cysteine-rich region, a transmembrane domain, and a variable cytoplasmic tail. We recently identified a novel member of this superfamily, ADAMDEC1 (decysin). Due to the partial lack of a disintegrin domain and the total lack of a cysteine-rich domain, this protein has been placed in a novel subclass of the ADAM gene family. We have investigated the gene structure of the human and mouse ADAMDEC1 and have revealed a metalloprotease gene cluster on human Chromosome 8p12 comprising ADAMDEC1, ADAM7, and ADAM28. Our results suggest that ADAMDEC1 has arisen by partial gene duplication from an ancestral gene at this locus and has acquired a novel function. ADAMDEC1 is expressed in the immune system, by dendritic cells and macrophages. The relatedness of ADAMDEC1, ADAM7, and ADAM28 suggests that these proteases share a similar function.},

keywords = {ADAM Proteins, Amino Acid Sequence, Animals, Base Sequence, Chromosomes, Evolution, Gene Dosage, Gene Duplication, Genetic, Human, Humans, Inbred BALB C, Macaca mulatta, Membrane Glycoproteins, Metalloendopeptidases, Mice, Molecular, Molecular Sequence Data, Multigene Family, Pair 8, Promoter Regions, Sequence Alignment, Team-Mueller},

pubstate = {published},

tppubtype = {article}

}

@article{mueller_mannose_2001,

title = {Mannose receptor ligand-positive cells express the metalloprotease decysin in the B cell follicle},

author = {C G Mueller and I Cremer and P E Paulet and S Niida and N Maeda and S Lebeque and W H Fridman and C Sautès-Fridman},

doi = {10.4049/jimmunol.167.9.5052},

issn = {0022-1767},

year  = {2001},

date = {2001-11-01},

journal = {Journal of Immunology (Baltimore, Md.: 1950)},

volume = {167},

number = {9},

pages = {5052--5060},

abstract = {Decysin, a gene encoding a disintegrin metalloprotease, is transcribed in human dendritic cells (DC) and germinal centers (GC). We have cloned its murine homologue and show that it is processed by the endoprotease furin before secretion of the catalytic domain. We have defined the cell types that express decysin in mouse spleen in the course of an immune response to T cell-dependent Ags. Like in humans, decysin is transcribed by activated CD11c(+) DC that enter the T cell zone from the marginal zone (MZ). In the GC, decysin is expressed by follicular DC and tingible body macrophages. In addition, a MZ cell population expresses decysin and appears to migrate into the B cell follicle. The majority of these follicle-homing cells express the mannose receptor ligand, a marker for the macrophage-like MZ metallophils. The follicle-homing cells are M-CSF dependent, as they are absent in op/op mice that lack functional M-CSF. This suggests that mannose receptor ligand(+) MZ metallophils differentiate into cells that migrate from the MZ into the B cell follicle. Decysin represents the first marker for this previously unrecognized cell population of the mouse spleen, which may represent a precursor for GCDC and may be specialized in the transport of unprocessed Ag from the MZ into developing GC.},

keywords = {ADAM Proteins, Amino Acid Sequence, Animals, B-Lymphocytes, C-Type, Cell Surface, Cloning, Dendritic Cells, Follicular, Germinal Center, Humans, Inbred BALB C, Lectins, ligands, Macrophage Colony-Stimulating Factor, Macrophages, Mannose-Binding Lectins, Metalloendopeptidases, Mice, Molecular, Molecular Sequence Data, Receptors, SPLEEN, Team-Mueller},

pubstate = {published},

tppubtype = {article}

}

@article{furrer_evidence_2001,

title = {Evidence of secondary structure by high-resolution magic angle spinning NMR spectroscopy of a bioactive peptide bound to different solid supports},

author = {J Furrer and M Piotto and M Bourdonneau and D Limal and G Guichard and K Elbayed and J Raya and J P Briand and A Bianco},

doi = {10.1021/ja003566w},

issn = {0002-7863},

year  = {2001},

date = {2001-01-01},

journal = {Journal of the American Chemical Society},

volume = {123},

number = {18},

pages = {4130--4138},

abstract = {The structure of the 19-amino acid peptide epitope, corresponding to the 141-159 sequence of capsid viral protein VP1 of foot-and-mouth disease virus (FMDV), bound to three different resins, namely, polystyrene-MBHA, PEGA, and POEPOP, has been determined by high-resolution magic angle spinning (HRMAS) NMR spectroscopy. A combination of homonuclear and heteronuclear bidimensional experiments was used for the complete peptide resonance assignment and the qualitative characterization of the peptide folding. The influence of the chemicophysical nature of the different polymers on the secondary structure of the covalently attached FMDV peptide was studied in detail. In the case of polystyrene-MBHA and polyacrylamide-PEGA resins, the analysis of the 2D spectra was hampered by missing signals and extensive overlaps, and only a propensity toward a peptide secondary structure could be derived from the assigned NOE correlations. When the FMDV peptide was linked to the polyoxyethylene-based POEPOP resin, it was found to adopt in dimethylformamide a helical conformation encompassing the C-terminal domain from residues 152 to 159. This conformation is very close to that of the free peptide previously analyzed in 2,2,2-trifluoroethanol. Our study clearly demonstrates that a regular helical structure can be adopted by a resin-bound bioactive peptide. Moreover, a change in the folding was observed when the same peptide-POEPOP conjugate was swollen in aqueous solution, displaying the same conformational features as the free peptide in water. The possibility of studying solid-supported ordered secondary structures by the HRMAS NMR technique in a wide range of solvents can be extended either to other biologically relevant peptides and proteins or to new synthetic oligomers.},

keywords = {Amino Acid Sequence, biomolecular, Capsid, Capsid Proteins, Epitopes, I2CT, Molecular Sequence Data, Nuclear Magnetic Resonance, Peptide Fragments, Plant, Protein Structure, Resins, Secondary, Solvents, Team-Bianco},

pubstate = {published},

tppubtype = {article}

}

@article{casimir_conformational_2000,

title = {Conformational restriction of the Tyr53 side-chain in the decapeptide HE},

author = {J R Casimir and K Iterbeke and W Van Den Nest and M C Trescol-Biémont and H Dumortier and S Muller and D Gerlier and C Rabourdin-Combe and D Tourwé and J Paris},

doi = {10.1034/j.1399-3011.2000.00777.x},

issn = {1397-002X},

year  = {2000},

date = {2000-12-01},

journal = {The Journal of Peptide Research: Official Journal of the American Peptide Society},

volume = {56},

number = {6},

pages = {398--408},

abstract = {A series of conformationally restricted analogs of the hen egg lysozyme (HEL) decapeptide 52-61 in which the conformationally flexible Tyr53 residue was replaced by several more constrained tyrosine and phenylalanine analogs was prepared. Among these tyrosine and phenylalanine analogs were 1,2,3,4-tetrahydro-7-hydroxyisoquinoline-3-carboxylic acid (Htc), 1,2,3,4-tetrahydroisoquinoline-3-carboxylic acid (Tic), 4-amino- 1,2,4,5-tetrahydro-8-hydroxy-2-benzazepine-3-one (Hba), 4-amino-1,2,4,5-tetrahydro-2-benzazepine-3-one (Aba), 2-amino-6-hydroxytetralin-2-carboxylic acid (Hat) and 2-amino-5-hydroxyindan-2-carboxylic acid (Hai) in which the rotations around Calpha-Cbeta and Cbeta-Cgamma were restricted because of cyclization of the side-chain to the backbone. Synthesis of Pht-Hba-Gly-OH using a modification of the Flynn and de Laszlo procedure is described. Analogs of beta-methyltyrosine (beta-MeTyr) in which the side-chains were biased to particular side-chain torsional angles because of substitution at the beta-hydrogens were also prepared. These analogs of HEL[52-61] peptide were tested for their ability to bind to the major histocompatibility complex class II I-Ak molecule and to be recognized in this context by two T-cell hybridomas, specific for the parent peptide HEL[52-61]. The data showed that the conformation and also the configuration of the Tyr53 residue influenced both the binding of the peptide to I-Ak and the recognition of the peptide/I-Ak complex by a T-cell receptor.},

keywords = {Amino Acid Sequence, Animals, Antigen, Antigen-Presenting Cells, B-Lymphocytes, Chemical, Chickens, Dumortier, I2CT, Major Histocompatibility Complex, Mice, Models, Molecular Sequence Data, Muramidase, Peptide Biosynthesis, Peptides, Phenylalanine, Protein Binding, Protein Conformation, Receptors, T-Cell, Team-Dumortier, Temperature, Tyrosine},

pubstate = {published},

tppubtype = {article}

}

@article{dumortier_b_2000,

title = {B and Ŧ cell responses to the spliceosomal heterogeneous nuclear ribonucleoproteins A2 and B1 in normal and lupus mice},

author = {H Dumortier and F Monneaux and B Jahn-Schmid and J P Briand and K Skriner and P L Cohen and J S Smolen and G Steiner and S Muller},

doi = {10.4049/jimmunol.165.4.2297},

issn = {0022-1767},

year  = {2000},

date = {2000-08-01},

journal = {Journal of Immunology (Baltimore, Md.: 1950)},

volume = {165},

number = {4},

pages = {2297--2305},

abstract = {Autoantibodies directed against spliceosomal heterogeneous nuclear ribonucleoproteins (hnRNPs) are a typical feature of rheumatoid arthritis, systemic lupus erythematosus, and mixed-connective tissue disease. With the aim of investigating a potential pathogenic role of these Abs, we have studied the Ab response to A2/B1 hnRNPs in different murine models of lupus. The specificity of anti-A2/B1 Abs was tested with a series of 14 overlapping synthetic peptides covering the region 1-206 of A2 that contains most of the epitopes recognized by patients' Abs. A major epitope recognized very early during the course of the disease by Abs from most of MRL lpr/lpr mice but not from other lupus mice and from mice of different MHC haplotypes immunized against B1 was identified in residues 50-70. This peptide contains a highly conserved sequence RGFGFVTF also present in other hnRNPs and small nuclear ribonucleoproteins. Abs reacting with a second A2 epitope identified in residues 35-55 were detectable several weeks later, suggesting an intramolecular B cell epitope spreading during the course of the disease. We identified several T cell epitopes within the region 35-175 that generated an effective Th cell response with IL-2 and IFN-gamma secretion in nonautoimmune CBA/J mice sharing the same MHC haplotype H-2k as MRL/lpr mice. None of the peptides stimulated T cells primed in vivo with B1. Because Abs to peptide 50-70 were detected significantly earlier than Abs reacting with other A2 peptides and the protein itself, it is possible that within the protein, this segment contains residues playing an initiator role in the induction of the anti-A2/B1 and antispliceosome Ab response.},

keywords = {Amino Acid Sequence, Animals, Autoantibodies, B-Lymphocytes, Dumortier, Epitope Mapping, Female, Heterogeneous Nuclear, Heterogeneous-Nuclear Ribonucleoprotein Group A-B, Heterogeneous-Nuclear Ribonucleoproteins, Humans, I2CT, Immunoglobulin G, Inbred BALB C, Inbred C57BL, Inbred CBA, Inbred MRL lpr, Injections, Lupus Nephritis, Lymphocyte Activation, Male, Mice, Molecular Sequence Data, Monneaux, Peptide Fragments, Recombinant Proteins, Ribonucleoproteins, RNA, Spliceosomes, Subcutaneous, T-Lymphocytes, Team-Dumortier, transgenic},

pubstate = {published},

tppubtype = {article}

}

@article{adamkewicz_purification_2000,

title = {Purification and enzymic properties of Mot1 ATPase, a regulator of basal transcription in the yeast Saccharomyces cerevisiae},

author = {J I Adamkewicz and C G Mueller and K E Hansen and W A Prud'homme and J Thorner},

doi = {10.1074/jbc.M002639200},

issn = {0021-9258},

year  = {2000},

date = {2000-07-01},

journal = {The Journal of Biological Chemistry},

volume = {275},

number = {28},

pages = {21158--21168},

abstract = {The 1867-residue Mot1 protein is a member of a superfamily of ATPases, some of which are helicases, that interact with protein-nucleic acid assemblies. Mot1 is an essential regulator of RNA polymerase II-dependent transcription in vivo and dissociates TATA box-binding protein (TBP)-DNA complexes in vitro. Mot1-(His)(6) was purified to apparent homogeneity from yeast extracts. The preparation efficiently dissociated TBP.TATA complexes, suggesting that no other protein or cofactor is required. Mot1 behaved as a non-globular monomer in hydrodynamic studies, and no association was detected between differentially tagged co-expressed Mot1 constructs. ATPase activity was stimulated about 10-fold by high ionic strength or alkaline pH, or by deletion of the N-terminal TBP-binding segment, suggesting that the N-terminal domain negatively regulates the C-terminal ATPase domain (Mot1C). Correspondingly, at moderate salt concentration, Mot1 ATPase (but not Mot1C) was stimulated textgreater/=10-fold by yeast TBP, suggesting that interaction with TBP relieves a conformational constraint in Mot1. Double- or single-stranded TATA-containing DNA did not affect ATPase activity of Mot1 or Mot1C, with or without TBP. Mot1 did not exhibit detectable helicase activity in strand displacement assays using substrates with flush ends or 5'- or 3'-overhangs. Mot1-catalyzed dissociation of TBP from DNA was not prevented by a psoralen cross-link positioned immediately preceding the TATA sequence. Thus, Mot1 most likely promotes release of TBP from TATA-containing DNA by causing a structural change in TBP itself, rather than by strand unwinding.},

keywords = {Adenosine Triphosphatases, Base Sequence, Chromatography, DNA Helicases, DNA-Binding Proteins, Fungal, Gel, Gene Expression Regulation, Genetic, Kinetics, Molecular Sequence Data, Molecular Weight, Osmolar Concentration, Recombinant Proteins, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, TATA Box, TATA-Binding Protein Associated Factors, TATA-Box Binding Protein, Team-Mueller, Transcription, Transcription Factors},

pubstate = {published},

tppubtype = {article}

}

@article{otten_sequence_1999,

title = {Sequence and functional analysis of the left-hand part of the Ŧ-region from the nopaline-type Ti plasmid, pTiC58.},

author = {L Otten and J Y Salomone and A Helfer and J Schmidt and P Hammann and P De Ruffray},

doi = {10.1023/a:1006370207379},

issn = {0167-4412 0167-4412},

year  = {1999},

date = {1999-12-01},

journal = {Plant molecular biology},

volume = {41},

number = {6},

pages = {765--776},

abstract = {The Agrobacterium tumefaciens nopaline strain C58 transfers a large, 29 kb T-DNA into plant cells during infection. Part of this DNA (the 'common DNA') is also found on the T-DNA of octopine strains, the remaining DNA is nopaline strain-specific. Up to now, only parts of the C58 T-DNA and related T37 T-DNA have been sequenced. We have sequenced the remainder of the nopaline-specific T-DNA (containing genes a to d) and acs to iaaM. Gene c codes for a new unknown T-DNA protein. Gene a is homologous to the agrocinopine synthase gene. Genes b, c', d and e are part of a larger family: they are related to the T-DNA genes 5, rolB, lso and 3'. Genes 5, rolB and lso induce or modify plant growth and have been called T-DNA oncogenes. Our studies show that gene 3' (located on the TR-DNA of octopine strains) is also oncogenic. Although the b-e T-DNA fragment from C58 and its individual genes lack growth-inducing activity, an a-acs deletion mutant was distinctly less virulent on Kalanchoe daigremontiana and showed reduced shoot formation on Kalanchoe tubiflora. Shoot formation could be restored by genes c and c' in co-infection experiments. Contrary to an earlier report, a C58 e gene deletion mutant was fully virulent on all plants tested.},

note = {Place: Netherlands},

keywords = {Agrobacterium tumefaciens/*genetics/pathogenicity, Bacterial/chemistry/*genetics, Bacterial/genetics, Chromosome Mapping, DNA, Gene Deletion, Genes, Genetic Complementation Test, Lycopersicon esculentum/genetics/microbiology, Medicinal/genetics/microbiology, Molecular Sequence Data, Mutation, Phylogeny, Plant Tumors/genetics/microbiology, Plants, Plasmids/chemistry/*genetics, PPSE, Sequence Analysis, Species Specificity, Tobacco/genetics/microbiology, Toxic, Virulence/genetics},

pubstate = {published},

tppubtype = {article}

}

@article{dumortier_at_1998,

title = {At least three linear regions but not the zinc-finger domain of U1C protein are exposed at the surface of the protein in solution and on the human spliceosomal U1 snRNP particle},

author = {H Dumortier and J Klein Gunnewiek and J P Roussel and Y van Aarssen and J P Briand and W J van Venrooij and S Muller},

doi = {10.1093/nar/26.23.5486},

issn = {0305-1048},

year  = {1998},

date = {1998-12-01},

journal = {Nucleic Acids Research},

volume = {26},

number = {23},

pages = {5486--5491},

abstract = {No structural information on U1C protein either in its free state or bound to the spliceosomal U1 small nuclear ribonucleoprotein (snRNP) particle is currently available. Using rabbit antibodies raised against a complete set of 15 U1C overlapping synthetic peptides (16-30 residues long) in different immunochemical tests, linear regions exposed at the surface of free and U1 snRNP-bound U1C were identified. Epitopes within at least three regions spanning residues 31-62, 85-103 and 116-159 were recognized on free and plastic-immobilized recombinant human U1C expressed in Escherichia coli, on in vitro translated U1C protein and on U1C bound to the U1 snRNP particle present in HeLa S100 extract. Using a zinc affinity labeling method, we further showed that the N-terminal U1C peptide containing a zinc-finger motif (peptide 5-34) effectively binds65Zn2+. The N-terminal region of U1C, which is functional in U1 snRNP assembly, is apparently not located at the surface of the U1 snRNP particle.},

keywords = {Amino Acid Sequence, Animals, Dumortier, HeLa Cells, Humans, I2CT, Molecular Sequence Data, Peptide Fragments, Protein Binding, Rabbits, Ribonucleoprotein, Ribonucleoproteins, Small Nuclear, Solutions, Spliceosomes, Team-Dumortier, U1 Small Nuclear, Zinc, Zinc Fingers},

pubstate = {published},

tppubtype = {article}

}

@article{meziere_vivo_1997,

title = {In vivo Ŧ helper cell response to retro-inverso peptidomimetics},

author = {C Mézière and M Viguier and H Dumortier and R Lo-Man and C Leclerc and J G Guillet and J P Briand and S Muller},

issn = {0022-1767},

year  = {1997},

date = {1997-10-01},

journal = {Journal of Immunology (Baltimore, Md.: 1950)},

volume = {159},

number = {7},

pages = {3230--3237},

abstract = {Peptide analogues containing reversed peptide bonds between each residue along the peptide sequence (retro-inverso modification) have been analyzed for their antigenic and in vivo immunogenic properties in the MHC II and Th cell response context. Two antigenic peptides were selected for this study, namely peptide 103-115 of poliovirus VP1, which is involved in the production of Abs that neutralize the infectivity of the virus, and peptide 435-446 from the third constant region of mouse heavy chain IgG2a allopeptide gamma 2ab, which mimics a corneal Ag implicated in autoimmune keratitis. In a competition assay performed in vitro using reference hybridomas of known MHC class II restriction, both retro-inverso analogues bound (although more weakly in our test) to I-Ad and/or I-Ed class II molecules. However, in both cases, this lower affinity was apparently largely compensated in vivo, as a T cell response (with IL-2 secretion), equivalent to that obtained with the wild-type peptides, was observed following immunization of BALB/c mice with the retro-inverso analogues. Moreover, these T cells proliferated and produced IL-2 in response to the cognate peptides. It is concluded that the T cell receptors of T cells primed in vivo with the retro-inverso analogues readily cross-react with parent and retro-inverso analogue-MHC complexes. The approach of using pseudopeptides containing changes involving the backbone, and not the orientation of side chains, may thus be promising to design potent immunogens for class II-restricted T cells.},

keywords = {Amino Acid Sequence, Animals, Antibodies, Antigen, Capsid, Capsid Proteins, Dumortier, Female, Helper-Inducer, Histocompatibility Antigens Class II, I2CT, Immunoglobulin Allotypes, Immunoglobulin G, Inbred BALB C, Injections, Intraperitoneal, Lymphocyte Activation, Mice, Molecular Sequence Data, Peptide Fragments, Poliovirus, Protein Binding, Receptors, T-Cell, T-Lymphocytes, Team-Dumortier, Viral},

pubstate = {published},

tppubtype = {article}

}

@article{halimi_comparison_1996,

title = {Comparison of two different methods using overlapping synthetic peptides for localizing linear B cell epitopes in the U1 snRNP-C autoantigen},

author = {H Halimi and H Dumortier and J P Briand and S Muller},

doi = {10.1016/s0022-1759(96)00171-8},

issn = {0022-1759},

year  = {1996},

date = {1996-11-01},

journal = {Journal of Immunological Methods},

volume = {199},

number = {1},

pages = {77--85},

abstract = {We have compared the performances of two different approaches using overlapping synthetic peptides to identify the location of linear epitopes of the U1 snRNP-C autoantigen. The first method was based on the use of 15 overlapping peptides (16-30 residue-long) synthesized using conventional Fmoc chemistry, removed from the resin by a standard cleavage procedure, and tested by ELISA after direct coating to polyvinyl microtiter plates. The second approach used a commercial kit (SPOT) to synthesize 75 overlapping decapeptides on cellulose membrane which were assayed by a direct immunoenzymatic test. Both standard and SPOTscan methods were evaluated with antibodies raised in rabbits against synthetic peptides of U1C and sera from patients with autoimmune diseases. In addition to inherent problems linked to the SPOT synthesis (in particular the impossibility of checking the quality of peptides), a number of limitations in the SPOTscan method were identified (e.g. a certain lack of sensitivity and, in one case, the complete lack of peptide reactivity due to the removal of charged end groups at both extremities). However, we found no background with sera from autoimmune patients in the SPOTscan and the antigenic maps obtained using the two approaches generally agreed. This study shows that the SPOTscan approach represents a simple, relatively non expensive and rapid method for initial screening to identify candidate sequences that may be dominant linear epitopes in a protein. Subsequent analysis and controls should include the preparation of conventionally synthesized peptides for formal immunochemical investigations.},

keywords = {Amino Acid Sequence, Autoantigens, B-Lymphocytes, Dumortier, Enzyme-Linked Immunosorbent Assay, Epitope Mapping, Humans, I2CT, Lupus Erythematosus, Molecular Sequence Data, Peptides, Ribonucleoprotein, Systemic, Team-Dumortier, U1 Small Nuclear},

pubstate = {published},

tppubtype = {article}

}