Genomes and Genes
Experts and Doctors on base sequence in Grenoble, Auvergne Rhône Alpes, France
Locale: Grenoble, Auvergne Rhône Alpes, France
Topic: base sequence
- Hartlein M, Frank R, Madern D. Nucleotide sequence of Escherichia coli valyl-tRNA synthetase gene valS. Nucleic Acids Res. 1987;15:9081-2 pubmed
- Leclerc M, Colbeau A, Cauvin B, Vignais P. Cloning and sequencing of the genes encoding the large and the small subunits of the H2 uptake hydrogenase (hup) of Rhodobacter capsulatus. Mol Gen Genet. 1988;214:97-107 pubmed..gigas. In the R. capsulatus hydrogenase the Cys residues (13 in the small subunit and 12 in the large subunit) were not arranged in the typical configuration found in [4Fe-4S] feredoxins...
- Frelet Barrand A, Boutigny S, Moyet L, Deniaud A, Seigneurin Berny D, Salvi D, et al. Lactococcus lactis, an alternative system for functional expression of peripheral and intrinsic Arabidopsis membrane proteins. PLoS ONE. 2010;5:e8746 pubmed publisher..Altogether, these data suggest that Lactococcus lactis might be an attractive system for the efficient and functional production of difficult plant membrane proteins. ..
- Escoffier J, Lee H, Yassine S, Zouari R, Martinez G, KaraouzÃ¨ne T, et al. Homozygous mutation of PLCZ1 leads to defective human oocyte activation and infertility that is not rescued by the WW-binding protein PAWP. Hum Mol Genet. 2016;25:878-91 pubmed publisher..This opens the door to structure-function studies to identify the conserved amino acids of the C2 domain that regulate the targeting of PLCZ1 and its selectivity for its lipid substrate(s). ..
- Boulay F, Tardif M, Brouchon L, Vignais P. The human N-formylpeptide receptor. Characterization of two cDNA isolates and evidence for a new subfamily of G-protein-coupled receptors. Biochemistry. 1990;29:11123-33 pubmed..The structural similarities observed with RDC1, a receptor isolated from a dog thyroid cDNA library, which shares weak homologies with other members of the family, suggests that the fMLP receptor is representative of a new subfamily. ..
- Uzan G, Frachet P, Lajmanovich A, Prandini M, Denarier E, Duperray A, et al. cDNA clones for human platelet GPIIb corresponding to mRNA from megakaryocytes and HEL cells. Evidence for an extensive homology to other Arg-Gly-Asp adhesion receptors. Eur J Biochem. 1988;171:87-93 pubmed
- Torki M, Mandaron P, Thomas F, Quigley F, Mache R, Falconet D. Differential expression of a polygalacturonase gene family in Arabidopsis thaliana. Mol Gen Genet. 1999;261:948-52 pubmed
- Vieille Grosjean I, Huber P. Transcription factor GATA-1 regulates human HOXB2 gene expression in erythroid cells. J Biol Chem. 1995;270:4544-50 pubmed..These findings suggest a regulatory hierarchy in which GATA-1 is upstream of the HOXB2 gene in erythroid cells. ..
- Scaramozzino N, Ferrier Rembert A, Favier A, Rothlisberger C, Richard S, Crance J, et al. Real-time PCR to identify variola virus or other human pathogenic orthopox viruses. Clin Chem. 2007;53:606-13 pubmed..Efforts are mounting to replenish the smallpox vaccine stocks, optimize diagnostic methods for poxviruses, and develop new antivirals against smallpox, because it is feared that variola virus might be used as a weapon of bioterrorism...
- Huber P, Dalmon J, Engiles J, Breviario F, Gory S, Siracusa L, et al. Genomic structure and chromosomal mapping of the mouse VE-cadherin gene (Cdh5). Genomics. 1996;32:21-8 pubmed
- Fieschi F, Niviere V, Fontecave M. Cys5 and Cys214 of NAD(P)H:flavin oxidoreductase from Escherichia coli are located in the active site. Eur J Biochem. 1996;237:870-5 pubmed..This strongly suggested that Cys5 and Cys214 are located at the flavin-binding site of Fre and that flavin can bind to the enzyme in the absence of NADPH. ..
- Brutscher B, Simorre J. Transverse relaxation optimized HCN experiment for nucleic acids: combining the advantages of TROSY and MQ spin evolution. J Biomol NMR. 2001;21:367-72 pubmed..The advantages of the MQ-TROSY-HCN experiment compared to the best previous implementations of HCN are demonstrated for a 33 nucleotide RNA aptamer...
- Seve M, Chimienti F, Devergnas S, Favier A. In silico identification and expression of SLC30 family genes: an expressed sequence tag data mining strategy for the characterization of zinc transporters' tissue expression. BMC Genomics. 2004;5:32 pubmed..The method presented herein provides a useful tool to complete gene families from sequencing programs and to produce preliminary expression data to select the proper biological samples for laboratory experimentation. ..
- Scaramozzino N, Crance J, Jouan A, DeBriel D, Stoll F, Garin D. Comparison of flavivirus universal primer pairs and development of a rapid, highly sensitive heminested reverse transcription-PCR assay for detection of flaviviruses targeted to a conserved region of the NS5 gene sequences. J Clin Microbiol. 2001;39:1922-7 pubmed..This technique was successfully performed with a cerebrospinal fluid sample from a patient hospitalized with West Nile virus encephalitis...
- Lobreaux S, Massenet O, Briat J. Iron induces ferritin synthesis in maize plantlets. Plant Mol Biol. 1992;19:563-75 pubmed..Ferritin mRNA accumulation was transient and particularly abundant in leaves, reaching a maximum at 24 h. The level of ferritin mRNA in roots was affected to a lesser extent than in leaves. ..
- Ben Fredj N, Grange J, Sadoul R, Richard S, Goldberg Y, Boyer V. Depolarization-induced translocation of the RNA-binding protein Sam68 to the dendrites of hippocampal neurons. J Cell Sci. 2004;117:1079-90 pubmed..These results support the possible involvement of Sam68 in the activity-dependent regulation of dendritic mRNAs. ..
- Kanzler B, Prin F, Thelu J, Dhouailly D. CHOXC-8 and CHOXD-13 expression in embryonic chick skin and cutaneous appendage specification. Dev Dyn. 1997;210:274-87 pubmed..These results strengthen the hypothesis that different homeobox genes play a significant role in specifying the regional identity of the different epidermal territories. ..
- Ben Khelifa M, Zouari R, Harbuz R, Halouani L, Arnoult C, Lunardi J, et al. A new AURKC mutation causing macrozoospermia: implications for human spermatogenesis and clinical diagnosis. Mol Hum Reprod. 2011;17:762-8 pubmed publisher..This diagnosis is important as the identification of AURKC mutations in patients indicates that all spermatozoa will be chromosomally abnormal and that ICSI should not be attempted. ..
- Barakate A, Martin W, Quigley F, Mache R. Characterization of a multigene family encoding an exopolygalacturonase in maize. J Mol Biol. 1993;229:797-801 pubmed..We estimate that 12 exopolygalacturonase genes exist in maize. None appear to be expressed at a detectable level in tissue other than those associated with pollen development. ..
- Toussaint B, Delic Attree I, Vignais P. Pseudomonas aeruginosa contains an IHF-like protein that binds to the algD promoter. Biochem Biophys Res Commun. 1993;196:416-421 pubmed..It is also demonstrated by gel retardation assays that P. aeruginosa IHF forms a stable complex with the algD promoter in vitro, an indication that the protein is involved in the regulation of algD gene expression in P. aeruginosa. ..
- Madern D, Pfister C, Zaccai G. Mutation at a single acidic amino acid enhances the halophilic behaviour of malate dehydrogenase from Haloarcula marismortui in physiological salts. Eur J Biochem. 1995;230:1088-95 pubmed..These results highlight the role of acidic amino acids in halophilic behaviour and are in agreement with a model in which these amino acids act cooperatively to organise hydrated ion binding to the protein...
- Carfi A, Pares S, Du e E, Galleni M, Duez C, Fr re J, et al. The 3-D structure of a zinc metallo-beta-lactamase from Bacillus cereus reveals a new type of protein fold. EMBO J. 1995;14:4914-21 pubmed..The structure shows that most of these residues are in the active site. Among these, aspartic acid 90 and histidine 210 participate in a proposed catalytic mechanism for beta-lactam hydrolysis...
- Quigley F, Brinkmann H, Martin W, Cerff R. Strong functional GC pressure in a light-regulated maize gene encoding subunit GAPA of chloroplast glyceraldehyde-3-phosphate dehydrogenase: implications for the evolution of GAPA pseudogenes. J Mol Evol. 1989;29:412-21 pubmed..A speculative model is presented explaining these observations in terms of a homologous recombination of genes with their reverse-transcribed pre-mRNAs. ..
- Eymery A, Callanan M, Vourc h C. The secret message of heterochromatin: new insights into the mechanisms and function of centromeric and pericentric repeat sequence transcription. Int J Dev Biol. 2009;53:259-68 pubmed publisher..The structure of the transcripts generated, the molecular mechanisms underlying their expression and their supposed functions will be discussed. ..
- Martinez P, Martin W, Cerff R. Structure, evolution and anaerobic regulation of a nuclear gene encoding cytosolic glyceraldehyde-3-phosphate dehydrogenase from maize. J Mol Biol. 1989;208:551-65 pubmed..In spite of its "typical" anaerobic promoter, the Gpc1 gene does not seem to be an anaerobic gene in vivo...
- Cannac Caffrey V, Hudry Clergeon G, Petillot Y, Gagnon J, Zaccai G, Franzetti B. The protein sequence of an archaeal catalase-peroxidase. Biochimie. 1998;80:1003-11 pubmed..Similarly to other soluble halophilic proteins, it shows the excess of acidic residues that has been associated with solvation in halophilic adaptation. ..
- El Refy A, Perazza D, Zekraoui L, Valay J, Bechtold N, Brown S, et al. The Arabidopsis KAKTUS gene encodes a HECT protein and controls the number of endoreduplication cycles. Mol Genet Genomics. 2003;270:403-14 pubmed..The KAK gene defines a monophylogenetic subgroup of HECT proteins that also contain Armadillo-like repeats. ..
- Brouillet S, Hoffmann P, Chauvet S, Salomon A, Chamboredon S, Sergent F, et al. Revisiting the role of hCG: new regulation of the angiogenic factor EG-VEGF and its receptors. Cell Mol Life Sci. 2012;69:1537-50 pubmed publisher..Altogether, these results demonstrate a new role for hCG in the regulation of EG-VEGF and its receptors, an emerging regulatory system in placental development. ..
- Moyroud E, Minguet E, Ott F, Yant L, Posé D, Monniaux M, et al. Prediction of regulatory interactions from genome sequences using a biophysical model for the Arabidopsis LEAFY transcription factor. Plant Cell. 2011;23:1293-306 pubmed publisher..Therefore, our work opens new avenues to deduce the structure of regulatory networks from mere inspection of genomic sequences. ..
- Duraffour S, Ishchenko A, Saparbaev M, Crance J, Garin D. Substrate specificity of homogeneous monkeypox virus uracil-DNA glycosylase. Biochemistry. 2007;46:11874-81 pubmed..Potential targets and strategies for combating pathogenic orthopoxviruses, including smallpox, are discussed...
- Lescuyer P, Martinez P, Lunardi J. YY1 and Sp1 activate transcription of the human NDUFS8 gene encoding the mitochondrial complex I TYKY subunit. Biochim Biophys Acta. 2002;1574:164-74 pubmed..Together with previous studies, our results indicate that YY1 and Sp1 control the expression of genes encoding proteins that are involved in almost all steps of the oxidative phosphorylation metabolism. ..
- Aguezzoul M, Andrieux A, Denarier E. Overlap of promoter and coding sequences in the mouse STOP gene (Mtap6). Genomics. 2003;81:623-7 pubmed..F-STOP mRNA transcription is regulated by a distinct promoter. A remarkable feature of this promoter is that it lies within coding sequences expressed in neuronal E- and N-STOP isoforms. ..
- Taberlet P, Gielly L, Pautou G, Bouvet J. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Mol Biol. 1991;17:1105-9 pubmed
- Aubert D, Chevillard M, Dorne A, Arlaud G, Herzog M. Expression patterns of GASA genes in Arabidopsis thaliana: the GASA4 gene is up-regulated by gibberellins in meristematic regions. Plant Mol Biol. 1998;36:871-83 pubmed..The GA-dependent meristem-specific expression pattern suggests that the GASA4 protein plays a role in dividing cells rather than in elongating cells. ..
- Vincent C, Borel F, Willison J, Leberman R, Hartlein M. Seryl-tRNA synthetase from Escherichia coli: functional evidence for cross-dimer tRNA binding during aminoacylation. Nucleic Acids Res. 1995;23:1113-8 pubmed..These results are in full agreement with the structural analysis of E. coli SerRS complexed with its cognate tRNA and provide functional evidence for the cross-dimer binding of tRNA in solution. ..
- Prandini M, Denarier E, Frachet P, Uzan G, Marguerie G. Isolation of the human platelet glycoprotein IIb gene and characterization of the 5' flanking region. Biochem Biophys Res Commun. 1988;156:595-601 pubmed..Upstream the transcription start site, two sequences are homologous to consensus binding sites of the nuclear factors SP1 and CP2. Two inverted repeats were also identified in this region. ..
- Boulay F, Tardif M, Brouchon L, Vignais P. Synthesis and use of a novel N-formyl peptide derivative to isolate a human N-formyl peptide receptor cDNA. Biochem Biophys Res Commun. 1990;168:1103-9 pubmed..The cDNA was 1.9 kb long with a 1050 bp open reading frame encoding a 350 residue protein. The hydropathy plot analysis revealed seven hydrophobic segments, a pattern quite similar to that of G protein-coupled receptors. ..
- Lescure A, Proudhon D, Pesey H, Ragland M, Theil E, Briat J. Ferritin gene transcription is regulated by iron in soybean cell cultures. Proc Natl Acad Sci U S A. 1991;88:8222-6 pubmed
- Bernaudat F, Frelet Barrand A, Pochon N, Dementin S, Hivin P, Boutigny S, et al. Heterologous expression of membrane proteins: choosing the appropriate host. PLoS ONE. 2011;6:e29191 pubmed publisher..The results highlight certain factors that should be considered when selecting an expression host. The decision aide provided should help both newcomers and old-hands to select the best system for their favourite membrane protein. ..
- Niogret M, Dubald M, Mandaron P, Mache R. Characterization of pollen polygalacturonase encoded by several cDNA clones in maize. Plant Mol Biol. 1991;17:1155-64 pubmed..PG-encoding genes from a small genomic family. Sequence analysis of three PG cDNA clones shows that they are closely related. The divergence of nucleotides between these three cDNA clones is 1%. They encode the same product. ..
- Anselme J, Hartlein M. Tyr-426 of the Escherichia coli asparaginyl-tRNA synthetase, an amino acid in a C-terminal conserved motif, is involved in ATP binding. FEBS Lett. 1991;280:163-6 pubmed..The replacement of this Tyr-426 by a Phe does not affect the kinetic behaviour of the enzyme. These data indicate that Tyr-426 is part of the ATP binding site. ..
- Roux Buisson N, Rendu J, Denjoy I, Guicheney P, Goldenberg A, David N, et al. Functional analysis reveals splicing mutations of the CASQ2 gene in patients with CPVT: implication for genetic counselling and clinical management. Hum Mutat. 2011;32:995-9 pubmed publisher..Moreover, our report of the first splicing abnormalities in CASQ2 caused by intronic mutation or synonymous change underlines the absolute necessity to perform extensive molecular analysis for genetic diagnosis and counseling of CPVT. ..
- Ythier D, Larrieu D, Binet R, Binda O, Brambilla C, Gazzeri S, et al. Sumoylation of ING2 regulates the transcription mediated by Sin3A. Oncogene. 2010;29:5946-56 pubmed publisher..Hence, sumoylation of ING2 enhances its binding to the Sin3A/HDAC complex and is required to regulate gene transcriptions. ..
- Anselme J, Hartlein M. Asparaginyl-tRNA synthetase from Escherichia coli has significant sequence homologies with yeast aspartyl-tRNA synthetase. Gene. 1989;84:481-5 pubmed
- Lajmanovich A, Ribeyron J, Florin A, Fournier A, Pasquier M, Duley S, et al. Identification, characterisation and regulation by CD40 activation of novel CD95 splice variants in CD95-apoptosis-resistant, human, B-cell non-Hodgkin's lymphoma. Exp Cell Res. 2009;315:3281-93 pubmed publisher..Thus, immune modulation of CD95 transcription and alternative splicing combined with enhanced engagement of mitochondrial death signalling offer potential for restoration of CD95 apoptosis sensitivity in B-NHLr...
- Boudet J, Chouquet A, Chahboune A, Giustini C, Joris B, Simorre J, et al. 1H, 13C and 15N resonance assignments of YajG, an Escherichia coli protein of unknown structure and function. Biomol NMR Assign. 2007;1:89-91 pubmed publisher..Located upstream in the same operon, is another 579-base-pair-long open reading frame encoding a putative lipoprotein YajG, whose nearly complete 1H,13C,15N assignments are reported here. ..
- Hoemann C, Bergeret E, Guichard A, Griffin Shea R. Alternative splicing of the Drosophila melanogaster rotundRacGAP gene. Gene. 1996;168:135-41 pubmed..rnRacGAP(1) is the predominant species in the testes and is expressed at a low level in the ovary and somatic tissues. rnRacGAP(2) is only very weakly expressed and is detectable solely in the testes. ..
- Chabre O, Portrat Doyen S, Chaffanjon P, Vivier J, Liakos P, Labat Moleur F, et al. Bilateral laparoscopic adrenalectomy for congenital adrenal hyperplasia with severe hypertension, resulting from two novel mutations in splice donor sites of CYP11B1. J Clin Endocrinol Metab. 2000;85:4060-8 pubmed..Thus, bilateral adrenalectomy in this patient allowed effective treatment of severe hypertension and helped in understanding the mechanisms and physiopathological consequences of two novel mutations of CYP11B1. ..
- Leiros I, Timmins J, Hall D, McSweeney S. Crystal structure and DNA-binding analysis of RecO from Deinococcus radiodurans. EMBO J. 2005;24:906-18 pubmed..Furthermore, drRecO was found to form a stable complex with RecR and to bind both single- and double-stranded DNA. Mutational analysis confirmed the existence of multiple DNA-binding sites within the protein. ..
- Raymond K, Bergeret E, Dagher M, Breton R, Griffin Shea R, Fauvarque M. The Rac GTPase-activating protein RotundRacGAP interferes with Drac1 and Dcdc42 signalling in Drosophila melanogaster. J Biol Chem. 2001;276:35909-16 pubmed..Finally, in a situation where Drac1 is constitutively activated, RotundRacGAP greatly reduces the ectopic expression of decapentaplegic, possibly by negatively regulating Dcdc42. ..
- Quigley F, Martin W, Cerff R. Intron conservation across the prokaryote-eukaryote boundary: structure of the nuclear gene for chloroplast glyceraldehyde-3-phosphate dehydrogenase from maize. Proc Natl Acad Sci U S A. 1988;85:2672-6 pubmed..J. (1984) EMBO J. 3, 1307-1310]. These results suggest that intron 3 is an archetypical relic of early GAPDH and alcohol dehydrogenase evolution, whereas introns 1 and 2 were implicated in the evolution of chloroplast transit peptides. ..