Champagne K S, Sissler M, Larrabee Y, Doublie S, Francklyn C S
Activation of the hetero-octameric ATP phosphoribosyl transferase through subunit interface rearrangement by a tRNA synthetase paralog Article de journal
Dans: J Biol Chem, vol. 280, no. 40, p. 34096-34104, 2005, ISBN: 16051603, (0021-9258 (Print) Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Extramural Research Support, FLORENTZ ATP Phosphoribosyltransferase/*metabolism Allosteric Regulation Amino Acyl-tRNA Synthetases DNA Mutational Analysis Enzyme Activation *Models, N.I.H., Non-P.H.S. Research Support, P.H.S., SISSLER, Structural Phosphates/metabolism Research Support, U.S. Gov't, Unité ARN
@article{,
title = {Activation of the hetero-octameric ATP phosphoribosyl transferase through subunit interface rearrangement by a tRNA synthetase paralog},
author = {K S Champagne and M Sissler and Y Larrabee and S Doublie and C S Francklyn},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16051603},
isbn = {16051603},
year = {2005},
date = {2005-01-01},
journal = {J Biol Chem},
volume = {280},
number = {40},
pages = {34096-34104},
abstract = {ATP phosphoribosyl transferase (ATP-PRT) joins ATP and 5-phosphoribosyl-1-pyrophosphate (PRPP) in a highly regulated reaction that initiates histidine biosynthesis. The unusual hetero-octameric version of ATP-PRT includes four HisG(S) catalytic subunits based on the periplasmic binding protein fold and four HisZ regulatory subunits that resemble histidyl-tRNA synthetases. Here, we present the first structure of a PRPP-bound ATP-PRT at 2.9 A and provide a structural model for allosteric activation based on comparisons with other inhibited and activated ATP-PRTs from both the hetero-octameric and hexameric families. The activated state of the octameric enzyme is characterized by an interstitial phosphate ion in the HisZ-HisG interface and new contacts between the HisZ motif 2 loop and the HisG(S) dimer interface. These contacts restructure the interface to recruit conserved residues to the active site, where they activate pyrophosphate to promote catalysis. Additionally, mutational analysis identifies the histidine binding sites within a region highly conserved between HisZ and the functional HisRS. Through the oligomerization and functional re-assignment of protein domains associated with aminoacylation and phosphate binding, the HisZ-HisG octameric ATP-PRT acquired the ability to initiate the synthesis of a key metabolic intermediate in an allosterically regulated fashion.},
note = {0021-9258 (Print)
Journal Article},
keywords = {Extramural Research Support, FLORENTZ ATP Phosphoribosyltransferase/*metabolism Allosteric Regulation Amino Acyl-tRNA Synthetases DNA Mutational Analysis Enzyme Activation *Models, N.I.H., Non-P.H.S. Research Support, P.H.S., SISSLER, Structural Phosphates/metabolism Research Support, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Rangan P, Masquida B, Westhof E, Woodson S A
Architecture and folding mechanism of the Azoarcus Group I Pre-tRNA Article de journal
Dans: J Mol Biol, vol. 339, no. 1, p. 41-51, 2004, ISBN: 15123419, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Azoarcus/enzymology/*genetics Base Sequence Binding Sites Exoribonucleases/metabolism Hydroxyl Radical/metabolism Introns/*genetics Magnesium/chemistry Models, Bacterial/*chemistry/genetics/*metabolism RNA, Ile/chemistry/*genetics Substrate Specificity Support, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA Precursors/*genetics RNA Splice Sites/genetics RNA Splicing RNA, Non-U.S. Gov't Support, P.H.S., Transfer, U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {Architecture and folding mechanism of the Azoarcus Group I Pre-tRNA},
author = {P Rangan and B Masquida and E Westhof and S A Woodson},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15123419},
isbn = {15123419},
year = {2004},
date = {2004-01-01},
journal = {J Mol Biol},
volume = {339},
number = {1},
pages = {41-51},
abstract = {Self-splicing RNAs must evolve to function in their specific exon context. The conformation of a group I pre-tRNA(ile) from the bacterium Azoarcus was probed by ribonuclease T(1) and hydroxyl radical cleavage, and by native gel electrophoresis. Biochemical data and three-dimensional models of the pre-tRNA showed that the tRNA is folded, and that the tRNA and intron sequences form separate tertiary domains. Models of the active site before steps 1 and 2 of the splicing reaction predict that exchange of the external G-cofactor and the 3'-terminal G is accomplished by a slight conformational change in P9.0 of the Azoarcus group I intron. Kinetic assays showed that the pre-tRNA folds in minutes, much more slowly than the intron alone. The dependence of the folding kinetics on Mg(2+) and the concentration of urea, and RNase T(1) experiments showed that formation of native pre-tRNA is delayed by misfolding of P3-P9, including mispairing between residues in P9 and the tRNA. Thus, although the intron and tRNA sequences form separate domains in the native pre-tRNA, their folding is coupled via metastable non-native base-pairs. This could help prevent premature processing of the 5' and 3' ends of unspliced pre-tRNA.},
note = {0022-2836
Journal Article},
keywords = {Azoarcus/enzymology/*genetics Base Sequence Binding Sites Exoribonucleases/metabolism Hydroxyl Radical/metabolism Introns/*genetics Magnesium/chemistry Models, Bacterial/*chemistry/genetics/*metabolism RNA, Ile/chemistry/*genetics Substrate Specificity Support, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA Precursors/*genetics RNA Splice Sites/genetics RNA Splicing RNA, Non-U.S. Gov't Support, P.H.S., Transfer, U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Mathy N, Pellegrini O, Serganov A, Patel D J, Ehresmann C, Portier C
Specific recognition of rpsO mRNA and 16S rRNA by Escherichia coli ribosomal protein S15 relies on both mimicry and site differentiation Article de journal
Dans: Mol Microbiol, vol. 52, no. 3, p. 661-675, 2004, ISBN: 15101974, (0950-382x Journal Article).
Résumé | Liens | BibTeX | Étiquettes: 16S/chemistry/genetics/*metabolism Recombinant Fusion Proteins/metabolism Ribosomal Proteins/chemistry/*genetics/*metabolism Sequence Alignment Support, Bacterial Models, EHRESMANN Amino Acid Sequence Base Sequence Escherichia coli Proteins/chemistry/genetics/*metabolism Gene Expression Regulation, Messenger/metabolism RNA, Molecular *Molecular Mimicry Molecular Sequence Data Mutagenesis, Non-U.S. Gov't Support, P.H.S., Ribosomal, Secondary RNA, Site-Directed Nucleic Acid Conformation Protein Structure, U.S. Gov't, Unité ARN
@article{,
title = {Specific recognition of rpsO mRNA and 16S rRNA by Escherichia coli ribosomal protein S15 relies on both mimicry and site differentiation},
author = {N Mathy and O Pellegrini and A Serganov and D J Patel and C Ehresmann and C Portier},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15101974},
isbn = {15101974},
year = {2004},
date = {2004-01-01},
journal = {Mol Microbiol},
volume = {52},
number = {3},
pages = {661-675},
abstract = {The ribosomal protein S15 binds to 16S rRNA, during ribosome assembly, and to its own mRNA (rpsO mRNA), affecting autocontrol of its expression. In both cases, the RNA binding site is bipartite with a common subsite consisting of a G*U/G-C motif. The second subsite is located in a three-way junction in 16S rRNA and in the distal part of a stem forming a pseudoknot in Escherichia coli rpsO mRNA. To determine the extent of mimicry between these two RNA targets, we determined which amino acids interact with rpsO mRNA. A plasmid carrying rpsO (the S15 gene) was mutagenized and introduced into a strain lacking S15 and harbouring an rpsO-lacZ translational fusion. Analysis of deregulated mutants shows that each subsite of rpsO mRNA is recognized by a set of amino acids known to interact with 16S rRNA. In addition to the G*U/G-C motif, which is recognized by the same amino acids in both targets, the other subsite interacts with amino acids also involved in contacts with helix H22 of 16S rRNA, in the region adjacent to the three-way junction. However, specific S15-rpsO mRNA interactions can also be found, probably with A(-46) in loop L1 of the pseudoknot, demonstrating that mimicry between the two targets is limited.},
note = {0950-382x
Journal Article},
keywords = {16S/chemistry/genetics/*metabolism Recombinant Fusion Proteins/metabolism Ribosomal Proteins/chemistry/*genetics/*metabolism Sequence Alignment Support, Bacterial Models, EHRESMANN Amino Acid Sequence Base Sequence Escherichia coli Proteins/chemistry/genetics/*metabolism Gene Expression Regulation, Messenger/metabolism RNA, Molecular *Molecular Mimicry Molecular Sequence Data Mutagenesis, Non-U.S. Gov't Support, P.H.S., Ribosomal, Secondary RNA, Site-Directed Nucleic Acid Conformation Protein Structure, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Levinger L, Oestreich I, Florentz C, Morl M
A pathogenesis-associated mutation in human mitochondrial tRNALeu(UUR) leads to reduced 3'-end processing and CCA addition Article de journal
Dans: J Mol Biol, vol. 337, no. 3, p. 535-544, 2004, ISBN: 15019775, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: FLORENTZ, FLORENTZ Human Kinetics Mitochondrial Diseases/*genetics Nucleic Acid Conformation *Point Mutation RNA/*genetics/physiology *RNA 3' End Processing RNA Nucleotidyltransferases/metabolism RNA, Leu/*genetics/physiology Support, Non-U.S. Gov't Support, P.H.S., Transfer, U.S. Gov't, Unité ARN
@article{,
title = {A pathogenesis-associated mutation in human mitochondrial tRNALeu(UUR) leads to reduced 3'-end processing and CCA addition},
author = {L Levinger and I Oestreich and C Florentz and M Morl},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15019775},
isbn = {15019775},
year = {2004},
date = {2004-01-01},
journal = {J Mol Biol},
volume = {337},
number = {3},
pages = {535-544},
abstract = {Point mutations in mitochondrial tRNAs can cause severe multisystemic disorders such as mitochondrial encephalomyopathy with lactic acidosis and stroke-like episodes (MELAS) and myoclonus epilepsy with ragged-red fibers (MERRF). Some of these mutations impair one or more steps of tRNA maturation and protein biosynthesis including 5'-end-processing, post-transcriptional base modification, structural stability, aminoacylation, and formation of tRNA-ribosomal complexes. tRNALeu(UUR), an etiologic hot spot for such diseases, harbors 20 of more than 90 disease-associated mutations described to date. Here, the pathogenesis-associated base substitutions A3243G, T3250C, T3271C, A3302G and C3303T within this tRNA were tested for their effects on endonucleolytic 3'-end processing and CCA addition at the tRNA 3'-terminus. Whereas mutations A3243G, A3302G and C3303T reduced the efficiency of 3'-end cleavage, only the C3303T substitution was a less efficient substrate for CCA addition. These results support the view that pathogenesis may be elicited through cumulative effects of tRNA mutations: a mutation can impede several pre-tRNA processing steps, with each such reduction contributing to the overall impairment of tRNA function.},
note = {0022-2836
Journal Article},
keywords = {FLORENTZ, FLORENTZ Human Kinetics Mitochondrial Diseases/*genetics Nucleic Acid Conformation *Point Mutation RNA/*genetics/physiology *RNA 3' End Processing RNA Nucleotidyltransferases/metabolism RNA, Leu/*genetics/physiology Support, Non-U.S. Gov't Support, P.H.S., Transfer, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Levinger L, Mörl M, Florentz C
Mitochondrial tRNA 3' end metabolism and human disease Article de journal
Dans: Nucleic Acids Res, vol. 32, no. 18, p. 5430-5441, 2004, ISBN: 15477393, (1362-4962 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: FLORENTZ, Non-U.S. Gov't Support, P.H.S., Transfer/chemistry/*genetics/*metabolism Support, U.S. Gov't, Unité ARN
@article{,
title = {Mitochondrial tRNA 3' end metabolism and human disease},
author = {L Levinger and M Mörl and C Florentz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15477393},
isbn = {15477393},
year = {2004},
date = {2004-01-01},
journal = {Nucleic Acids Res},
volume = {32},
number = {18},
pages = {5430-5441},
abstract = {Over 150 mutations in the mitochondrial genome have been shown to be associated with human disease. Remarkably, two-thirds of them are found in tRNA genes, which constitute only one-tenth of the mitochondrial genome. A total of 22 tRNAs punctuate the genome and are produced together with 11 mRNAs and 2 rRNAs from long polycistronic primary transcripts with almost no spacers. Pre-tRNAs thus require precise endonucleolytic excision. Furthermore, the CCA triplet which forms the 3' end of all tRNAs is not encoded, but must be synthesized by the CCA-adding enzyme after 3' end cleavage. Amino acid attachment to the CCA of mature tRNA is performed by aminoacyl-tRNA synthetases, which, like the preceding processing enzymes, are nuclear-encoded and imported into mitochondria. Here, we critically review the effectiveness and reliability of evidence obtained from reactions with in vitro transcripts that pathogenesis-associated mutant mitochondrial tRNAs can lead to deficiencies in tRNA 3' end metabolism (3' end cleavage, CCA addition and aminoacylation) toward an understanding of molecular mechanisms underlying human tRNA disorders. These defects probably contribute, individually and cumulatively, to the progression of human mitochondrial diseases.},
note = {1362-4962
Journal Article
Review
Review, Tutorial},
keywords = {FLORENTZ, Non-U.S. Gov't Support, P.H.S., Transfer/chemistry/*genetics/*metabolism Support, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Wilhelm F. X., Wilhelm M., Gabriel A.
Extension and cleavage of the polypurine tract plus-strand primer by Ty1 reverse transcriptase Article de journal
Dans: J Biol Chem, vol. 278, no. 48, p. 47678-84, 2003, (0021-9258 Journal Article).
Résumé | BibTeX | Étiquettes: Base, Calf, Data, DNA, DNA/chemistry, Genetic, Gov't, H, Messenger/metabolism, Models, Molecular, Non-U.S., P.H.S., Polymerase/*chemistry, Primers, Proteins/chemistry, Purines/*chemistry, Recombinant, Replication, Retroelements/*genetics, Ribonuclease, RNA, RNA-Directed, RNA/chemistry, Sequence, Support, Templates, Thymus/chemistry, U.S., Viral
@article{,
title = {Extension and cleavage of the polypurine tract plus-strand primer by Ty1 reverse transcriptase},
author = { F. X. Wilhelm and M. Wilhelm and A. Gabriel},
year = {2003},
date = {2003-01-01},
journal = {J Biol Chem},
volume = {278},
number = {48},
pages = {47678-84},
abstract = {Using hybrid RNA/DNA substrates containing the polypurine tract (PPT) plus-strand primer, we have examined the interaction between the Ty1 reverse transcriptase (RT) and the plus-strand initiation complex. We show here that, although the PPT sequence is relatively resistant to RNase H cleavage, it can be cleaved internally by the polymerase-independent RNase H activity of Ty1 RT. Alternatively, this PPT can be used to initiate plus-strand DNA synthesis. We demonstrate that cleavage at the PPT/DNA junction occurs only after at least 9 nucleotides are extended. Cleavage leaves a nick between the RNA primer and the nascent plus-strand DNA. We show that Ty1 RT has a strand displacement activity beyond a gap but that the PPT is not efficiently re-utilized in vitro for another round of DNA synthesis after a first plus-strand DNA has been synthesized and cleaved at the PPT/U3 junction.},
note = {0021-9258
Journal Article},
keywords = {Base, Calf, Data, DNA, DNA/chemistry, Genetic, Gov't, H, Messenger/metabolism, Models, Molecular, Non-U.S., P.H.S., Polymerase/*chemistry, Primers, Proteins/chemistry, Purines/*chemistry, Recombinant, Replication, Retroelements/*genetics, Ribonuclease, RNA, RNA-Directed, RNA/chemistry, Sequence, Support, Templates, Thymus/chemistry, U.S., Viral},
pubstate = {published},
tppubtype = {article}
}
Yang H, Jossinet F, Leontis N, Chen L, Westbrook J, Berman H, Westhof E
Tools for the automatic identification and classification of RNA base pairs Article de journal
Dans: Nucleic Acids Res, vol. 31, no. 13, p. 3450-3460, 2003, ISBN: 12824344, (1362-4962 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Algorithms Base Pairing Base Sequence Computer Graphics Data Interpretation, Molecular Nucleic Acid Conformation RNA/*chemistry/classification *Software Support, Non-P.H.S. Support, Non-U.S. Gov't Support, Nucleic Acid Internet Models, P.H.S., Statistical Databases, U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {Tools for the automatic identification and classification of RNA base pairs},
author = {H Yang and F Jossinet and N Leontis and L Chen and J Westbrook and H Berman and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12824344},
isbn = {12824344},
year = {2003},
date = {2003-01-01},
journal = {Nucleic Acids Res},
volume = {31},
number = {13},
pages = {3450-3460},
abstract = {Three programs have been developed to aid in the classification and visualization of RNA structure. BPViewer provides a web interface for displaying three-dimensional (3D) coordinates of individual base pairs or base pair collections. A web server, RNAview, automatically identifies and classifies the types of base pairs that are formed in nucleic acid structures by various combinations of the three edges, Watson-Crick, Hoogsteen and the Sugar edge. RNAView produces two-dimensional (2D) diagrams of secondary and tertiary structure in either Postscript, VRML or RNAML formats. The application RNAMLview can be used to rearrange various parts of the RNAView 2D diagram to generate a standard representation (like the cloverleaf structure of tRNAs) or any layout desired by the user. A 2D diagram can be rapidly reformatted using RNAMLview since all the parts of RNA (like helices and single strands) are dynamically linked while moving the selected parts. With the base pair annotation and the 2D graphic display, RNA motifs are rapidly identified and classified. A survey has been carried out for 41 unique structures selected from the NDB database. The statistics for the occurrence of each edge and of each of the 12 bp families are given for the combinations of the four bases: A, G, U and C. The program also allows for visualization of the base pair interactions by using a symbolic convention previously proposed for base pairs. The web servers for BPViewer and RNAview are available at http://ndbserver.rutgers.edu/services/. The application RNAMLview can also be downloaded from this site. The 2D diagrams produced by RNAview are available for RNA structures in the Nucleic Acid Database (NDB) at http://ndbserver.rutgers.edu/atlas/.},
note = {1362-4962
Journal Article},
keywords = {Algorithms Base Pairing Base Sequence Computer Graphics Data Interpretation, Molecular Nucleic Acid Conformation RNA/*chemistry/classification *Software Support, Non-P.H.S. Support, Non-U.S. Gov't Support, Nucleic Acid Internet Models, P.H.S., Statistical Databases, U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Tsai H Y, Masquida B, Biswas R, Westhof E, Gopalan V
Molecular modeling of the three-dimensional structure of the bacterial RNase P holoenzyme Article de journal
Dans: J Mol Biol, vol. 325, no. 4, p. 661-675, 2003, ISBN: 12507471, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Amino Acid Sequence Base Sequence Catalytic Domain Computer Simulation Cysteine/chemistry DNA Footprinting DNA, Bacterial/chemistry/genetics/metabolism RNA, Bacterial/genetics Edetic Acid Endoribonucleases/*chemistry/genetics/metabolism Escherichia coli/*enzymology/genetics Evolution, Catalytic/*chemistry/genetics/metabolism Ribonuclease P Support, Molecular Ferrous Compounds Holoenzymes/chemistry/genetics/metabolism Hydroxyl Radical/chemistry Models, Molecular Molecular Sequence Data Mutagenesis, Non-P.H.S. Support, P.H.S., Site-Directed Nucleic Acid Conformation Protein Subunits RNA, U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {Molecular modeling of the three-dimensional structure of the bacterial RNase P holoenzyme},
author = {H Y Tsai and B Masquida and R Biswas and E Westhof and V Gopalan},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12507471},
isbn = {12507471},
year = {2003},
date = {2003-01-01},
journal = {J Mol Biol},
volume = {325},
number = {4},
pages = {661-675},
abstract = {Bacterial ribonuclease P (RNase P), an enzyme involved in tRNA maturation, consists of a catalytic RNA subunit and a protein cofactor. Comparative phylogenetic analysis and molecular modeling have been employed to derive secondary and tertiary structure models of the RNA subunits from Escherichia coli (type A) and Bacillus subtilis (type B) RNase P. The tertiary structure of the protein subunit of B.subtilis and Staphylococcus aureus RNase P has recently been determined. However, an understanding of the structure of the RNase P holoenzyme (i.e. the ribonucleoprotein complex) is lacking. We have now used an EDTA-Fe-based footprinting approach to generate information about RNA-protein contact sites in E.coli RNase P. The footprinting data, together with results from other biochemical and biophysical studies, have furnished distance constraints, which in turn have enabled us to build three-dimensional models of both type A and B versions of the bacterial RNase P holoenzyme in the absence and presence of its precursor tRNA substrate. These models are consistent with results from previous studies and provide both structural and mechanistic insights into the functioning of this unique catalytic RNP complex.},
note = {0022-2836
Journal Article},
keywords = {Amino Acid Sequence Base Sequence Catalytic Domain Computer Simulation Cysteine/chemistry DNA Footprinting DNA, Bacterial/chemistry/genetics/metabolism RNA, Bacterial/genetics Edetic Acid Endoribonucleases/*chemistry/genetics/metabolism Escherichia coli/*enzymology/genetics Evolution, Catalytic/*chemistry/genetics/metabolism Ribonuclease P Support, Molecular Ferrous Compounds Holoenzymes/chemistry/genetics/metabolism Hydroxyl Radical/chemistry Models, Molecular Molecular Sequence Data Mutagenesis, Non-P.H.S. Support, P.H.S., Site-Directed Nucleic Acid Conformation Protein Subunits RNA, U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Rangan P, Masquida B, Westhof E, Woodson S A
Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 100, no. 4, p. 1574-1579, 2003, ISBN: 12574513, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Azoarcus/*enzymology Base Sequence Introns Magnesium/chemistry Models, Catalytic/*chemistry/genetics Support, Molecular Molecular Sequence Data Nucleic Acid Conformation *Protein Folding Protein Structure, Non-U.S. Gov't Support, P.H.S., Tertiary RNA, U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {Assembly of core helices and rapid tertiary folding of a small bacterial group I ribozyme},
author = {P Rangan and B Masquida and E Westhof and S A Woodson},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12574513},
isbn = {12574513},
year = {2003},
date = {2003-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {100},
number = {4},
pages = {1574-1579},
abstract = {Compact but non-native intermediates have been implicated in the hierarchical folding of several large RNAs, but there is little information on their structure. In this article, ribonuclease and hydroxyl radical cleavage protection assays showed that base pairing of core helices stabilize a compact state of a small group I ribozyme from Azoarcus pre-tRNA(ile). Base pairing of the ribozyme core requires 10-fold less Mg(2+) than stable tertiary interactions, indicating that assembly of helices in the catalytic core represents a distinct phase that precedes the formation of native tertiary structure. Tertiary folding occurs in <100 ms at 37 degrees C. Such rapid folding is unprecedented among group I ribozymes and illustrates the association between structural complexity and folding time. A 3D model of the Azoarcus ribozyme was constructed by identifying homologous sequence motifs in rRNA. The model reveals distinct structural features, such as a large interface between the P4-P6 and P3-P9 domains, that may explain the unusual stability of the Azoarcus ribozyme and the cooperativity of folding.},
note = {0027-8424
Journal Article},
keywords = {Azoarcus/*enzymology Base Sequence Introns Magnesium/chemistry Models, Catalytic/*chemistry/genetics Support, Molecular Molecular Sequence Data Nucleic Acid Conformation *Protein Folding Protein Structure, Non-U.S. Gov't Support, P.H.S., Tertiary RNA, U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Levinger L, Giege R, Florentz C
Pathology-related substitutions in human mitochondrial tRNA(Ile) reduce precursor 3' end processing efficiency in vitro Article de journal
Dans: Nucleic Acids Res, vol. 31, no. 7, p. 1904-1912, 2003, ISBN: 12655007, (1362-4962 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence DNA, FLORENTZ, Ile/*genetics/metabolism Support, Mitochondrial/*genetics Endoribonucleases/metabolism Hela Cells Human Kinetics Molecular Sequence Data Mutation RNA Precursors/genetics/metabolism *RNA Processing, Non-U.S. Gov't Support, P.H.S., Post-Transcriptional RNA, Transfer, U.S. Gov't, Unité ARN
@article{,
title = {Pathology-related substitutions in human mitochondrial tRNA(Ile) reduce precursor 3' end processing efficiency in vitro},
author = {L Levinger and R Giege and C Florentz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12655007},
isbn = {12655007},
year = {2003},
date = {2003-01-01},
journal = {Nucleic Acids Res},
volume = {31},
number = {7},
pages = {1904-1912},
abstract = {The human mitochondrial genome encodes 22 tRNAs interspersed among the two rRNAs and 11 mRNAs, often without spacers, suggesting that tRNAs must be efficiently excised. Numerous maternally transmitted diseases and syndromes arise from mutations in mitochondrial tRNAs, likely due to defect(s) in tRNA metabolism. We have systematically explored the effect of pathogenic mutations on tRNA(Ile) precursor 3' end maturation in vitro by 3'-tRNase. Strikingly, four pathogenic tRNA(Ile) mutations reduce 3'-tRNase processing efficiency (V(max) / K(M)) to approximately 10-fold below that of wild-type, principally due to lower V(max). The structural impact of mutations was sought by secondary structure probing and wild-type tRNA(Ile) precursor was found to fold into a canonical cloverleaf. Among the mutant tRNA(Ile) precursors with the greatest 3' end processing deficiencies, only G4309A displays a secondary structure substantially different from wild-type, with changes in the T domain proximal to the substitution. Reduced efficiency of tRNA(Ile) precursor 3' end processing, in one case associated with structural perturbations, could thus contribute to human mitochondrial diseases caused by mutant tRNAs.},
note = {1362-4962
Journal Article},
keywords = {Base Sequence DNA, FLORENTZ, Ile/*genetics/metabolism Support, Mitochondrial/*genetics Endoribonucleases/metabolism Hela Cells Human Kinetics Molecular Sequence Data Mutation RNA Precursors/genetics/metabolism *RNA Processing, Non-U.S. Gov't Support, P.H.S., Post-Transcriptional RNA, Transfer, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Leontis N B, Westhof E
Analysis of RNA motifs Article de journal
Dans: Curr Opin Struct Biol, vol. 13, no. 3, p. 300-308, 2003, ISBN: 12831880, (0959-440x Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: *Base Pairing Binding Sites Magnetic Resonance Imaging *Nucleic Acid Conformation RNA/*chemistry RNA, Chloroplast/chemistry Support, P.H.S., U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {Analysis of RNA motifs},
author = {N B Leontis and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12831880},
isbn = {12831880},
year = {2003},
date = {2003-01-01},
journal = {Curr Opin Struct Biol},
volume = {13},
number = {3},
pages = {300-308},
abstract = {RNA motifs are directed and ordered stacked arrays of non-Watson-Crick base pairs forming distinctive foldings of the phosphodiester backbones of the interacting RNA strands. They correspond to the 'loops' - hairpin, internal and junction - that intersperse the Watson-Crick two-dimensional helices as seen in two-dimensional representations of RNA structure. RNA motifs mediate the specific interactions that induce the compact folding of complex RNAs. RNA motifs also constitute specific protein or ligand binding sites. A given motif is characterized by all the sequences that fold into essentially identical three-dimensional structures with the same ordered array of isosteric non-Watson-Crick base pairs. It is therefore crucial, when analyzing a three-dimensional RNA structure in order to identify and compare motifs, to first classify its non-Watson-Crick base pairs geometrically.},
note = {0959-440x
Journal Article
Review
Review, Tutorial},
keywords = {*Base Pairing Binding Sites Magnetic Resonance Imaging *Nucleic Acid Conformation RNA/*chemistry RNA, Chloroplast/chemistry Support, P.H.S., U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Gottar Marie, Gobert Vanessa, Michel Tatiana, Belvin Marcia, Duyk Geoffrey, Hoffmann Jules A, Ferrandon Dominique, Royet Julien
The Drosophila immune response against Gram-negative bacteria is mediated by a peptidoglycan recognition protein Article de journal
Dans: Nature, vol. 416, p. 640–644, 2002, ISBN: 0028-0836.
Résumé | Liens | BibTeX | Étiquettes: Animal, Anti-Infective Agents/metabolism, Carrier Proteins/biosynthesis/genetics/*immunology, Drosophila melanogaster/genetics/*immunology/*microbiology, Drosophila Proteins/genetics/metabolism, Epistasis, Female, ferrandon, Genes, Genetic, Genetic Predisposition to Disease, Gram-Negative Bacteria/*immunology/physiology, hoffmann, Human, Insect/genetics, M3i, Messenger/genetics/metabolism, Mutation, Non-U.S. Gov't, P.H.S., Phenotype, RNA, Signal Transduction, Support, Survival Rate, Transgenes/genetics, U.S. Gov't
@article{gottar_drosophila_2002b,
title = {The Drosophila immune response against Gram-negative bacteria is mediated by a peptidoglycan recognition protein},
author = {Marie Gottar and Vanessa Gobert and Tatiana Michel and Marcia Belvin and Geoffrey Duyk and Jules A Hoffmann and Dominique Ferrandon and Julien Royet},
doi = {10.1038/nature734},
isbn = {0028-0836},
year = {2002},
date = {2002-03-01},
journal = {Nature},
volume = {416},
pages = {640--644},
abstract = {The antimicrobial defence of Drosophila relies largely on the challenge-induced synthesis of an array of potent antimicrobial peptides by the fat body. The defence against Gram-positive bacteria and natural fungal infections is mediated by the Toll signalling pathway, whereas defence against Gram-negative bacteria is dependent on the Immune deficiency (IMD) pathway. Loss-of-function mutations in either pathway reduce the resistance to corresponding infections. The link between microbial infections and activation of these two pathways has remained elusive. The Toll pathway is activated by Gram-positive bacteria through a circulating Peptidoglycan recognition protein (PGRP-SA). PGRPs appear to be highly conserved from insects to mammals, and the Drosophila genome contains 13 members. Here we report a mutation in a gene coding for a putative transmembrane protein, PGRP-LC, which reduces survival to Gram-negative sepsis but has no effect on the response to Gram-positive bacteria or natural fungal infections. By genetic epistasis, we demonstrate that PGRP-LC acts upstream of the imd gene. The data on PGRP-SA with respect to the response to Gram-positive infections, together with the present report, indicate that the PGRP family has a principal role in sensing microbial infections in Drosophila.},
keywords = {Animal, Anti-Infective Agents/metabolism, Carrier Proteins/biosynthesis/genetics/*immunology, Drosophila melanogaster/genetics/*immunology/*microbiology, Drosophila Proteins/genetics/metabolism, Epistasis, Female, ferrandon, Genes, Genetic, Genetic Predisposition to Disease, Gram-Negative Bacteria/*immunology/physiology, hoffmann, Human, Insect/genetics, M3i, Messenger/genetics/metabolism, Mutation, Non-U.S. Gov't, P.H.S., Phenotype, RNA, Signal Transduction, Support, Survival Rate, Transgenes/genetics, U.S. Gov't},
pubstate = {published},
tppubtype = {article}
}
Mohr S., Leikauf G. D., Keith G., Rihn B. H.
Microarrays as cancer keys: an array of possibilities Article de journal
Dans: J Clin Oncol, vol. 20, no. 14, p. 3165-75, 2002, (0732-183x Journal Article Review Review, Tutorial).
Résumé | BibTeX | Étiquettes: (Genetics), *Gene, *Oligonucleotide, *Sequence, Aberrations, Analysis, Analysis/methods, Animals, Array, Chromosome, DNA/methods, Expression, Genotype, Gov't, Human, Mutation, Neoplasms/*genetics, Neoplastic, Oncogenes/*genetics, P.H.S., Polymorphism, Profiling/methods, Proteome/genetics, Regulation, Sequence, Support, U.S.
@article{,
title = {Microarrays as cancer keys: an array of possibilities},
author = { S. Mohr and G. D. Leikauf and G. Keith and B. H. Rihn},
year = {2002},
date = {2002-01-01},
journal = {J Clin Oncol},
volume = {20},
number = {14},
pages = {3165-75},
abstract = {Malignant transformation results from accumulation of genetic and epigenetic events. Functional studies of cancer will be crucial to our understanding of its complexity and polymorphism. There is no doubt that emerging genomic and proteomic technologies will facilitate such investigations. Microarray technology is a new and efficient approach to extract data of biomedical relevance for a wide range of applications. In cancer research, it will provide high-throughput and valuable insights into differences in an individual's tumor as compared with constitutional DNA, mRNA expression, and protein expression and activity. Across individuals, comparisons could provide tissue-specific disease signatures that provide diagnosis based on hundreds of informative genes. The resulting product should be a wealth of tumor-associated and tumor-specific biomarkers, which may help in cancer etiology, diagnosis, and therapy and ultimately lead to "molecular nosology" of cancers. This review highlights the recent developments in microarray technologies in cancer research, focuses on the results obtained so far, and describes the eventual use of microarray technology for clinical applications.},
note = {0732-183x
Journal Article
Review
Review, Tutorial},
keywords = {(Genetics), *Gene, *Oligonucleotide, *Sequence, Aberrations, Analysis, Analysis/methods, Animals, Array, Chromosome, DNA/methods, Expression, Genotype, Gov't, Human, Mutation, Neoplasms/*genetics, Neoplastic, Oncogenes/*genetics, P.H.S., Polymorphism, Profiling/methods, Proteome/genetics, Regulation, Sequence, Support, U.S.},
pubstate = {published},
tppubtype = {article}
}
Wilhelm M., Fishman J. A., Pontikis R., Aubertin A. M., Wilhelm F. X.
Susceptibility of recombinant porcine endogenous retrovirus reverse transcriptase to nucleoside and non-nucleoside inhibitors Article de journal
Dans: Cell Mol Life Sci, vol. 59, no. 12, p. 2184-90, 2002, (1420-682x Journal Article).
Résumé | BibTeX | Étiquettes: Acid, Amino, Animals, Calf, Chloride/metabolism, Chlorides/metabolism, Cloning, Compounds/metabolism, Data, DNA, DNA-Directed, endogenous, Gov't, H, Human, Inhibitors/*pharmacology, Magnesium, Manganese, Molecular, Non-U.S., Nucleosides/chemistry/*metabolism, P.H.S., Polymerase/chemistry/genetics/*metabolism, Polymerase/metabolism, Proteins/metabolism, Recombinant, Retroviruses/*enzymology, Reverse, Ribonuclease, RNA-Directed, Sequence, Sodium, structure, Support, Swine, Thymus/metabolism, Transcriptase, U.S.
@article{,
title = {Susceptibility of recombinant porcine endogenous retrovirus reverse transcriptase to nucleoside and non-nucleoside inhibitors},
author = { M. Wilhelm and J. A. Fishman and R. Pontikis and A. M. Aubertin and F. X. Wilhelm},
year = {2002},
date = {2002-01-01},
journal = {Cell Mol Life Sci},
volume = {59},
number = {12},
pages = {2184-90},
abstract = {Transplantation of organs, tissues or cells from pigs to humans could be a potential solution to the shortage of human organs for transplantation. Porcine endogenous retroviruses (PERVs) remain a major safety concern for porcine xenotransplantation. Thus, finding drugs that could be used as virological prophylaxis (or therapy) against PERV replication would be desirable. One of the most effective ways to block retroviral multiplication is to inhibit the enzyme reverse transcriptase (RT) which catalyzes the reverse transcription of viral RNA to proviral double-stranded DNA. We report here the cloning and expression of PERV RT and its susceptibility to several inhibitors. Our data demonstrate PERV susceptibility in vitro to the triphosphorylated nucleoside analog of zidovudine (AZT) and to ddGTP and to a lesser extent to ddTTP but almost no susceptibility to the non-nucleoside RT inhibitors tested.},
note = {1420-682x
Journal Article},
keywords = {Acid, Amino, Animals, Calf, Chloride/metabolism, Chlorides/metabolism, Cloning, Compounds/metabolism, Data, DNA, DNA-Directed, endogenous, Gov't, H, Human, Inhibitors/*pharmacology, Magnesium, Manganese, Molecular, Non-U.S., Nucleosides/chemistry/*metabolism, P.H.S., Polymerase/chemistry/genetics/*metabolism, Polymerase/metabolism, Proteins/metabolism, Recombinant, Retroviruses/*enzymology, Reverse, Ribonuclease, RNA-Directed, Sequence, Sodium, structure, Support, Swine, Thymus/metabolism, Transcriptase, U.S.},
pubstate = {published},
tppubtype = {article}
}
Waugh A, Gendron P, Altman R, Brown J W, Case D, Gautheret D, Harvey S C, Leontis N, Westbrook J, Westhof E, Zuker M, Major F
RNAML: a standard syntax for exchanging RNA information Article de journal
Dans: RNA, vol. 8, no. 6, p. 707-717, 2002, ISBN: 12088144, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: *Databases, Non-P.H.S. Support, Non-U.S. Gov't Support, Nucleic Acid *Nucleic Acid Conformation Programming Languages RNA/*chemistry Support, P.H.S., U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {RNAML: a standard syntax for exchanging RNA information},
author = {A Waugh and P Gendron and R Altman and J W Brown and D Case and D Gautheret and S C Harvey and N Leontis and J Westbrook and E Westhof and M Zuker and F Major},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12088144},
isbn = {12088144},
year = {2002},
date = {2002-01-01},
journal = {RNA},
volume = {8},
number = {6},
pages = {707-717},
abstract = {Analyzing a single data set using multiple RNA informatics programs often requires a file format conversion between each pair of programs, significantly hampering productivity. To facilitate the interoperation of these programs, we propose a syntax to exchange basic RNA molecular information. This RNAML syntax allows for the storage and the exchange of information about RNA sequence and secondary and tertiary structures. The syntax permits the description of higher level information about the data including, but not restricted to, base pairs, base triples, and pseudoknots. A class-oriented approach allows us to represent data common to a given set of RNA molecules, such as a sequence alignment and a consensus secondary structure. Documentation about experiments and computations, as well as references to journals and external databases, are included in the syntax. The chief challenge in creating such a syntax was to determine the appropriate scope of usage and to ensure extensibility as new needs will arise. The syntax complies with the eXtensible Markup Language (XML) recommendations, a widely accepted standard for syntax specifications. In addition to the various generic packages that exist to read and interpret XML formats, an XML processor was developed and put in the open-source MC-Core library for nucleic acid and protein structure computer manipulation.},
note = {1355-8382
Journal Article},
keywords = {*Databases, Non-P.H.S. Support, Non-U.S. Gov't Support, Nucleic Acid *Nucleic Acid Conformation Programming Languages RNA/*chemistry Support, P.H.S., U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Mohr S, Leikauf G D, Keith G, Rihn B H
Microarrays as cancer keys: an array of possibilities Article de journal
Dans: J Clin Oncol, vol. 20, no. 14, p. 3165-3175, 2002, ISBN: 12118031, (0732-183x Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: Animals Chromosome Aberrations *Gene Expression Profiling/methods *Gene Expression Regulation, DNA/methods Support, Neoplastic Genotype Human Mutation Neoplasms/*genetics *Oligonucleotide Array Sequence Analysis/methods Oncogenes/*genetics Polymorphism (Genetics) Proteome/genetics *Sequence Analysis, P.H.S., U.S. Gov't, Unité ARN
@article{,
title = {Microarrays as cancer keys: an array of possibilities},
author = {S Mohr and G D Leikauf and G Keith and B H Rihn},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12118031},
isbn = {12118031},
year = {2002},
date = {2002-01-01},
journal = {J Clin Oncol},
volume = {20},
number = {14},
pages = {3165-3175},
abstract = {Malignant transformation results from accumulation of genetic and epigenetic events. Functional studies of cancer will be crucial to our understanding of its complexity and polymorphism. There is no doubt that emerging genomic and proteomic technologies will facilitate such investigations. Microarray technology is a new and efficient approach to extract data of biomedical relevance for a wide range of applications. In cancer research, it will provide high-throughput and valuable insights into differences in an individual's tumor as compared with constitutional DNA, mRNA expression, and protein expression and activity. Across individuals, comparisons could provide tissue-specific disease signatures that provide diagnosis based on hundreds of informative genes. The resulting product should be a wealth of tumor-associated and tumor-specific biomarkers, which may help in cancer etiology, diagnosis, and therapy and ultimately lead to "molecular nosology" of cancers. This review highlights the recent developments in microarray technologies in cancer research, focuses on the results obtained so far, and describes the eventual use of microarray technology for clinical applications.},
note = {0732-183x
Journal Article
Review
Review, Tutorial},
keywords = {Animals Chromosome Aberrations *Gene Expression Profiling/methods *Gene Expression Regulation, DNA/methods Support, Neoplastic Genotype Human Mutation Neoplasms/*genetics *Oligonucleotide Array Sequence Analysis/methods Oncogenes/*genetics Polymorphism (Genetics) Proteome/genetics *Sequence Analysis, P.H.S., U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Leontis N B, Stombaugh J, Westhof E
Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules Article de journal
Dans: Biochimie, vol. 84, no. 9, p. 961-973, 2002, ISBN: 12458088, (0300-9084 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bacterial/*chemistry/genetics RNA, Base Pairing Base Sequence Catalytic Domain Conserved Sequence Databases, Factual Models, Molecular *Nucleic Acid Conformation RNA, Non-P.H.S. Support, P.H.S., Ribosomal/*chemistry/genetics Sequence Alignment Support, U.S. Gov't, Unité ARN, WESTHOF
@article{,
title = {Motif prediction in ribosomal RNAs Lessons and prospects for automated motif prediction in homologous RNA molecules},
author = {N B Leontis and J Stombaugh and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12458088},
isbn = {12458088},
year = {2002},
date = {2002-01-01},
journal = {Biochimie},
volume = {84},
number = {9},
pages = {961-973},
abstract = {The traditional way to infer RNA secondary structure involves an iterative process of alignment and evaluation of covariation statistics between all positions possibly involved in basepairing. Watson-Crick basepairs typically show covariations that score well when examples of two or more possible basepairs occur. This is not necessarily the case for non-Watson-Crick basepairing geometries. For example, for sheared (trans Hoogsteen/Sugar edge) pairs, one base is highly conserved (always A or mostly A with some C or U), while the other can vary (G or A and sometimes C and U as well). RNA motifs consist of ordered, stacked arrays of non-Watson-Crick basepairs that in the secondary structure representation form hairpin or internal loops, multi-stem junctions, and even pseudoknots. Although RNA motifs occur recurrently and contribute in a modular fashion to RNA architecture, it is usually not apparent which bases interact and whether it is by edge-to-edge H-bonding or solely by stacking interactions. Using a modular sequence-analysis approach, recurrent motifs related to the sarcin-ricin loop of 23S RNA and to loop E from 5S RNA were predicted in universally conserved regions of the large ribosomal RNAs (16S- and 23S-like) before the publication of high-resolution, atomic-level structures of representative examples of 16S and 23S rRNA molecules in their native contexts. This provides the opportunity to evaluate the predictive power of motif-level sequence analysis, with the goal of automating the process for predicting RNA motifs in genomic sequences. The process of inferring structure from sequence by constructing accurate alignments is a circular one. The crucial link that allows a productive iteration of motif modeling and realignment is the comparison of the sequence variations for each putative pair with the corresponding isostericity matrix to determine which basepairs are consistent both with the sequence and the geometrical data.},
note = {0300-9084
Journal Article},
keywords = {Bacterial/*chemistry/genetics RNA, Base Pairing Base Sequence Catalytic Domain Conserved Sequence Databases, Factual Models, Molecular *Nucleic Acid Conformation RNA, Non-P.H.S. Support, P.H.S., Ribosomal/*chemistry/genetics Sequence Alignment Support, U.S. Gov't, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Wilhelm M., Uzun O., Mules E. H., Gabriel A., Wilhelm F. X.
Polypurine tract formation by Ty1 RNase H Article de journal
Dans: J Biol Chem, vol. 276, no. 50, p. 47695-701, 2001, (0021-9258 Journal Article).
Résumé | BibTeX | Étiquettes: *Purines, *Retroelements, Base, Binding, Calf, Data, DNA, DNA/metabolism, Factors, Gov't, H, Hydrolysis, Molecular, Mutation, Non-U.S., P.H.S., Polymerase/*chemistry/*metabolism, Primers/pharmacology, Protein, Proteins/metabolism, Recombinant, Ribonuclease, RNA-Directed, RNA/metabolism, Sequence, Sites, Support, Thymus/*chemistry/*genetics/metabolism, time, U.S.
@article{,
title = {Polypurine tract formation by Ty1 RNase H},
author = { M. Wilhelm and O. Uzun and E. H. Mules and A. Gabriel and F. X. Wilhelm},
year = {2001},
date = {2001-01-01},
journal = {J Biol Chem},
volume = {276},
number = {50},
pages = {47695-701},
abstract = {To better understand the mechanism by which Ty1 RNase H creates the polypurine tract (PPT) primer, we have demonstrated the polymerase-dependent hydrolytic activity of Ty1 reverse transcriptase (RT) during minus-strand synthesis. Using RNase H and polymerase mutants of the recombinant Ty1 RT protein, we show that the two domains of Ty1 RT can act independently of one another. Our results indicate that RNA/DNA substrates containing a short RNA PPT, which serve as primers for plus-strand DNA synthesis, are relatively resistant to RNase H cleavage. RNA substrates with a correct 5' end but with 3' end extending beyond the plus-strand initiation site were cleaved specifically to generate the correct 3' end of the PPT. Using long RNA/DNA duplexes containing the PPT, we show that Ty1 RT is able to make specific internal cleavages that could generate the plus-strand primer with correct 5' and 3' ends. Long RNA/DNA duplexes with mutations in the PPT or in a U-rich region upstream of the PPT, which abolish plus-strand initiation in vivo, were not cleaved specifically at the 5' end of the PPT. Our work demonstrates that the in vitro enzyme can recapitulate key processes that control proper replication in vivo.},
note = {0021-9258
Journal Article},
keywords = {*Purines, *Retroelements, Base, Binding, Calf, Data, DNA, DNA/metabolism, Factors, Gov't, H, Hydrolysis, Molecular, Mutation, Non-U.S., P.H.S., Polymerase/*chemistry/*metabolism, Primers/pharmacology, Protein, Proteins/metabolism, Recombinant, Ribonuclease, RNA-Directed, RNA/metabolism, Sequence, Sites, Support, Thymus/*chemistry/*genetics/metabolism, time, U.S.},
pubstate = {published},
tppubtype = {article}
}
Webb A E, Rose M A, Westhof E, Weeks K M
Protein-dependent transition states for ribonucleoprotein assembly Article de journal
Dans: J Mol Biol, vol. 309, no. 5, p. 1087-1100, 2001, ISBN: 11399081, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Allosteric Site Base Sequence Catalysis Catalytic Domain Fungal Proteins/*metabolism Hydroxyl Radical/metabolism Introns/genetics Iodine/metabolism Kinetics Models, Catalytic/chemistry/genetics/metabolism RNA-Binding Proteins/*metabolism Ribonucleoproteins/chemistry/*genetics/*metabolism Saccharomyces cerevisiae/enzymology/genetics *Saccharomyces cerevisiae Proteins Support, Molecular Neurospora crassa *Nucleic Acid Conformation Protein Binding RNA/chemistry/genetics/metabolism RNA Splicing/*genetics RNA Stability RNA, Non-U.S. Gov't Support, P.H.S., U.S. Gov't, Unité ARN
@article{,
title = {Protein-dependent transition states for ribonucleoprotein assembly},
author = {A E Webb and M A Rose and E Westhof and K M Weeks},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11399081},
isbn = {11399081},
year = {2001},
date = {2001-01-01},
journal = {J Mol Biol},
volume = {309},
number = {5},
pages = {1087-1100},
abstract = {Native folding and splicing by the Saccharomyces cerevisiae mitochondrial bI5 group I intron RNA is facilitated by both the S. cerevisiae CBP2 and Neurospora crassa CYT-18 protein cofactors. Both protein-bI5 RNA complexes splice at similar rates, suggesting that the RNA active site structure is similar in both ribonucleoproteins. In contrast, the two proteins assemble with the bI5 RNA by distinct mechanisms and bind opposing, but partially overlapping, sides of the group I intron catalytic core. Assembly with CBP2 is limited by a slow, unimolecular RNA folding step characterized by a negligible activation enthalpy. We show that assembly with CYT-18 shows four distinctive features. (1) CYT-18 binds stably to the bI5 RNA at the diffusion controlled limit, but assembly to a catalytically active RNA structure is still limited by RNA folding, as visualized directly using time-resolved footprinting. (2) This mechanism of rapid stable protein binding followed by subsequent assembly steps has a distinctive kinetic signature: the apparent ratio of k(off) to k(on), determined in a partitioning experiment, differs from the equilibrium K(d) by a large factor. (3) Assembly with CYT-18 is characterized by a large activation enthalpy, consistent with a rate limiting conformational rearrangement. (4) Because assembly from the kinetically trapped state is faster at elevated temperature, we can identify conditions where CYT-18 accelerates (catalyzes) bI5 RNA folding relative to assembly with CBP2.},
note = {0022-2836
Journal Article},
keywords = {Allosteric Site Base Sequence Catalysis Catalytic Domain Fungal Proteins/*metabolism Hydroxyl Radical/metabolism Introns/genetics Iodine/metabolism Kinetics Models, Catalytic/chemistry/genetics/metabolism RNA-Binding Proteins/*metabolism Ribonucleoproteins/chemistry/*genetics/*metabolism Saccharomyces cerevisiae/enzymology/genetics *Saccharomyces cerevisiae Proteins Support, Molecular Neurospora crassa *Nucleic Acid Conformation Protein Binding RNA/chemistry/genetics/metabolism RNA Splicing/*genetics RNA Stability RNA, Non-U.S. Gov't Support, P.H.S., U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Tzou P, Ohresser S, Ferrandon Dominique, Capovilla Maria, Reichhart Jean-Marc, Lemaitre Bruno, Hoffmann Jules A, Imler Jean-Luc
Tissue-specific inducible expression of antimicrobial peptide genes in Drosophila surface epithelia Article de journal
Dans: Immunity, vol. 13, p. 737–48., 2000, ISSN: 1074-7613.
Résumé | BibTeX | Étiquettes: *Genes, Animal, Anti-Infective Agents/*immunology/metabolism, Drosophila/genetics/*immunology, ferrandon, Gene Expression Regulation/*immunology, Genes, Glycoside Hydrolases/immunology, hoffmann, Human, imler, Insect, Insect Proteins/genetics/immunology, M3i, Non-U.S. Gov't, Organ Specificity, P.H.S., reichhart, Reporter, Support, Transfection, U.S. Gov't
@article{tzou_tissue-specific_2000b,
title = {Tissue-specific inducible expression of antimicrobial peptide genes in Drosophila surface epithelia},
author = {P Tzou and S Ohresser and Dominique Ferrandon and Maria Capovilla and Jean-Marc Reichhart and Bruno Lemaitre and Jules A Hoffmann and Jean-Luc Imler},
issn = {1074-7613},
year = {2000},
date = {2000-01-01},
journal = {Immunity},
volume = {13},
pages = {737--48.},
abstract = {The production of antimicrobial peptides is an important aspect of host defense in multicellular organisms. In Drosophila, seven antimicrobial peptides with different spectra of activities are synthesized by the fat body during the immune response and secreted into the hemolymph. Using GFP reporter transgenes, we show here that all seven Drosophila antimicrobial peptides can be induced in surface epithelia in a tissue-specific manner. The imd gene plays a critical role in the activation of this local response to infection. In particular, drosomycin expression, which is regulated by the Toll pathway during the systemic response, is regulated by imd in the respiratory tract, thus demonstrating the existence of distinct regulatory mechanisms for local and systemic induction of antimicrobial peptide genes in Drosophila.},
keywords = {*Genes, Animal, Anti-Infective Agents/*immunology/metabolism, Drosophila/genetics/*immunology, ferrandon, Gene Expression Regulation/*immunology, Genes, Glycoside Hydrolases/immunology, hoffmann, Human, imler, Insect, Insect Proteins/genetics/immunology, M3i, Non-U.S. Gov't, Organ Specificity, P.H.S., reichhart, Reporter, Support, Transfection, U.S. Gov't},
pubstate = {published},
tppubtype = {article}
}
Perreau V. M., Keith G., Holmes W. M., Przykorska A., Santos M. A., Tuite M. F.
The Candida albicans CUG-decoding ser-tRNA has an atypical anticodon stem-loop structure Article de journal
Dans: J Mol Biol, vol. 293, no. 5, p. 1039-53, 1999, (0022-2836 Journal Article).
Résumé | BibTeX | Étiquettes: *Nucleic, Acid, albicans/*genetics, Anticodon/*chemistry/*genetics/metabolism, Base, Candida, cerevisiae/genetics, Code/genetics, Conformation, Evolution, Fungal/chemistry/genetics/metabolism, Genetic, Gov't, Imidazoles/metabolism, Lead/metabolism, Methylation, Methyltransferases/metabolism, Molecular, Mutation/genetics, Non-P.H.S., Non-U.S., Nucleosides/genetics/metabolism, P.H.S., Ribonucleases/metabolism, RNA, Saccharomyces, Sequence, Ser/*chemistry/*genetics/metabolism, Solutions, Support, Transfer, tRNA, U.S.
@article{,
title = {The Candida albicans CUG-decoding ser-tRNA has an atypical anticodon stem-loop structure},
author = { V. M. Perreau and G. Keith and W. M. Holmes and A. Przykorska and M. A. Santos and M. F. Tuite},
year = {1999},
date = {1999-01-01},
journal = {J Mol Biol},
volume = {293},
number = {5},
pages = {1039-53},
abstract = {In many Candida species, the leucine CUG codon is decoded by a tRNA with two unusual properties: it is a ser-tRNA and, uniquely, has guanosine at position 33 (G33). Using a combination of enzymatic (V1 RNase, RnI nuclease) and chemical (Pb(2+), imidazole) probing of the native Candida albicans ser-tRNACAG, we demonstrate that the overall tertiary structure of this tRNA resembles that of a ser-tRNA rather than a leu-tRNA, except within the anticodon arm where there is considerable disruption of the anticodon stem. Using non-modified in vitro transcripts of the C. albicans ser-tRNACAG carrying G, C, U or A at position 33, we demonstrate that it is specifically a G residue at this position that induces the atypical anticodon stem structure. Further quantitative evidence for an unusual structure in the anticodon arm of the G33-tRNA is provided by the observed change in kinetics of methylation of the G at position 37, by purified Escherichia coli m(1)G37 methyltransferase. We conclude that the anticodon arm distortion, induced by a guanosine base at position 33 in the anticodon loop of this novel tRNA, results in reduced decoding ability which has facilitated the evolution of this tRNA without extinction of the species encoding it.},
note = {0022-2836
Journal Article},
keywords = {*Nucleic, Acid, albicans/*genetics, Anticodon/*chemistry/*genetics/metabolism, Base, Candida, cerevisiae/genetics, Code/genetics, Conformation, Evolution, Fungal/chemistry/genetics/metabolism, Genetic, Gov't, Imidazoles/metabolism, Lead/metabolism, Methylation, Methyltransferases/metabolism, Molecular, Mutation/genetics, Non-P.H.S., Non-U.S., Nucleosides/genetics/metabolism, P.H.S., Ribonucleases/metabolism, RNA, Saccharomyces, Sequence, Ser/*chemistry/*genetics/metabolism, Solutions, Support, Transfer, tRNA, U.S.},
pubstate = {published},
tppubtype = {article}
}
Bergdoll M., Eltis L. D., Cameron A. D., Dumas P., Bolin J. T.
All in the family: structural and evolutionary relationships among three modular proteins with diverse functions and variable assembly Article de journal
Dans: Protein Sci, vol. 7, no. 8, p. 1661-70, 1998, (0961-8368 Journal Article).
Résumé | BibTeX | Étiquettes: *Acetyltransferases, *Evolution, Acid, Amino, Bacterial, Burkholderia/*chemistry, Crystallography, Data, Genetic, Gov't, Homology, Human, Lactoylglutathione, Lyase/*chemistry, Models, Molecular, Non-U.S., Oxygenases/chemistry, P.H.S., Phylogeny, Protein, Proteins/*chemistry, Secondary, Sequence, structure, Support, U.S., X-Ray
@article{,
title = {All in the family: structural and evolutionary relationships among three modular proteins with diverse functions and variable assembly},
author = { M. Bergdoll and L. D. Eltis and A. D. Cameron and P. Dumas and J. T. Bolin},
year = {1998},
date = {1998-01-01},
journal = {Protein Sci},
volume = {7},
number = {8},
pages = {1661-70},
abstract = {The crystal structures of three proteins of diverse function and low sequence similarity were analyzed to evaluate structural and evolutionary relationships. The proteins include a bacterial bleomycin resistance protein, a bacterial extradiol dioxygenase, and human glyoxalase I. Structural comparisons, as well as phylogenetic analyses, strongly indicate that the modern family of proteins represented by these structures arose through a rich evolutionary history that includes multiple gene duplication and fusion events. These events appear to be historically shared in some cases, but parallel and historically independent in others. A significant early event is proposed to be the establishment of metal-binding in an oligomeric ancestor prior to the first gene fusion. Variations in the spatial arrangements of homologous modules are observed that are consistent with the structural principles of three-dimensional domain swapping, but in the unusual context of the formation of larger monomers from smaller dimers or tetramers. The comparisons support a general mechanism for metalloprotein evolution that exploits the symmetry of a homooligomeric protein to originate a metal binding site and relies upon the relaxation of symmetry, as enabled by gene duplication, to establish and refine specific functions.},
note = {0961-8368
Journal Article},
keywords = {*Acetyltransferases, *Evolution, Acid, Amino, Bacterial, Burkholderia/*chemistry, Crystallography, Data, Genetic, Gov't, Homology, Human, Lactoylglutathione, Lyase/*chemistry, Models, Molecular, Non-U.S., Oxygenases/chemistry, P.H.S., Phylogeny, Protein, Proteins/*chemistry, Secondary, Sequence, structure, Support, U.S., X-Ray},
pubstate = {published},
tppubtype = {article}
}
Gabus C., Ficheux D., Rau M., Keith G., Sandmeyer S., Darlix J. L.
The yeast Ty3 retrotransposon contains a 5'-3' bipartite primer-binding site and encodes nucleocapsid protein NCp9 functionally homologous to HIV-1 NCp7 Article de journal
Dans: EMBO J, vol. 17, no. 16, p. 4873-80, 1998, (0261-4189 Journal Article).
Résumé | BibTeX | Étiquettes: *Capsid, *Retroelements, Acid, Base, Binding, Capsid/*genetics, cerevisiae/*genetics, dimerization, gag/*genetics, Gene, Gov't, Homology, Met/genetics/*metabolism, Non-U.S., Nucleic, P.H.S., Products, Proteins, RNA, Saccharomyces, Sequence, Sites, Support, Transfer, U.S.
@article{,
title = {The yeast Ty3 retrotransposon contains a 5'-3' bipartite primer-binding site and encodes nucleocapsid protein NCp9 functionally homologous to HIV-1 NCp7},
author = { C. Gabus and D. Ficheux and M. Rau and G. Keith and S. Sandmeyer and J. L. Darlix},
year = {1998},
date = {1998-01-01},
journal = {EMBO J},
volume = {17},
number = {16},
pages = {4873-80},
abstract = {Retroviruses, including HIV-1 and the distantly related yeast retroelement Ty3, all encode a nucleoprotein required for virion structure and replication. During an in vitro comparison of HIV-1 and Ty3 nucleoprotein function in RNA dimerization and cDNA synthesis, we discovered a bipartite primer-binding site (PBS) for Ty3 composed of sequences located at opposite ends of the genome. Ty3 cDNA synthesis requires the 3' PBS for primer tRNAiMet annealing to the genomic RNA, and the 5' PBS, in cis or in trans, as the reverse transcription start site. Ty3 RNA alone is unable to dimerize, but formation of dimeric tRNAiMet bound to the PBS was found to direct dimerization of Ty3 RNA-tRNAiMet. Interestingly, HIV-1 nucleocapsid protein NCp7 and Ty3 NCp9 were interchangeable using HIV-1 and Ty3 RNA template-primer systems. Our findings impact on the understanding of non-canonical reverse transcription as well as on the use of Ty3 systems to screen for anti-NCp7 drugs.},
note = {0261-4189
Journal Article},
keywords = {*Capsid, *Retroelements, Acid, Base, Binding, Capsid/*genetics, cerevisiae/*genetics, dimerization, gag/*genetics, Gene, Gov't, Homology, Met/genetics/*metabolism, Non-U.S., Nucleic, P.H.S., Products, Proteins, RNA, Saccharomyces, Sequence, Sites, Support, Transfer, U.S.},
pubstate = {published},
tppubtype = {article}
}
Yusupova G, Lanchy J M, Yusupov M, Keith G, Grice S F Le, Ehresmann C, Ehresmann B, Marquet R
Primer selection by HIV-1 reverse transcriptase on RNA-tRNA(3Lys) and DNA-tRNA(3Lys) hybrids Article de journal
Dans: J Mol Biol, vol. 261, no. 3, p. 315-321, 1996, ISBN: 8780773, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence DNA, Lys/genetics/*metabolism RNA, MARQUET, Non-U.S. Gov't Support, P.H.S., Post-Transcriptional RNA, Transfer, U.S. Gov't, Unité ARN, Viral/genetics HIV-1/*enzymology/genetics HIV-1 Reverse Transcriptase Human Molecular Sequence Data *RNA Processing, Viral/genetics RNA-Directed DNA Polymerase/genetics/*metabolism Support
@article{,
title = {Primer selection by HIV-1 reverse transcriptase on RNA-tRNA(3Lys) and DNA-tRNA(3Lys) hybrids},
author = {G Yusupova and J M Lanchy and M Yusupov and G Keith and S F Le Grice and C Ehresmann and B Ehresmann and R Marquet},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8780773},
isbn = {8780773},
year = {1996},
date = {1996-01-01},
journal = {J Mol Biol},
volume = {261},
number = {3},
pages = {315-321},
abstract = {During reverse transcription of the genomic RNA of human immunodeficiency virus type 1 (HIV-1) into double-stranded DNA, reverse transcriptase (RT) must accommodate RNA-RNA, DNA-RNA, RNA-DNA and DNA-DNA hybrids as primer-template. In this study, we examined extension of RNA-tRNA3Lys, and DNA-tRNA3Lys complexes by HIV-1 RT. When the 3' end of tRNA3Lys is annealed to oligoribonucleotides, tRNA3Lys, but not the complementary RNAs, is extended by HIV-1 RT, indicating that tRNA3Lys is efficiently used as primer and RNA as template. An opposite primer usage is observed when tRNA3Lys is annealed to complementary oligodeoxyribonucleotides. In this case, the oligodeoxyribonucleotides are efficiently used as primer and tRNA3Lys as template. This result indicates that the nature of nucleic acid bound to tRNA3Lys determines which strand of the RNA-tRNA3Lys and DNA-tRNA3Lys hybrids is extended by HIV-1 RT. When an oligoribonucleotide is annealed to an unmodified transcript of tRNA3Lys, both nucleic acids are extended by HIV-1 RT, indicating that specific selection of tRNA3Lys as primer requires the post-transcriptional modifications of tRNA3Lys.},
note = {0022-2836
Journal Article},
keywords = {Base Sequence DNA, Lys/genetics/*metabolism RNA, MARQUET, Non-U.S. Gov't Support, P.H.S., Post-Transcriptional RNA, Transfer, U.S. Gov't, Unité ARN, Viral/genetics HIV-1/*enzymology/genetics HIV-1 Reverse Transcriptase Human Molecular Sequence Data *RNA Processing, Viral/genetics RNA-Directed DNA Polymerase/genetics/*metabolism Support},
pubstate = {published},
tppubtype = {article}
}
Westhof E, Wesolowski D, Altman S
Mapping in three dimensions of regions in a catalytic RNA protected from attack by an Fe(II)-EDTA reagent Article de journal
Dans: J Mol Biol, vol. 258, no. 4, p. 600-613, 1996, ISBN: 8636995, (0022-2836 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bacterial Proteins/chemistry/metabolism Base Sequence Coenzymes/*chemistry/drug effects Computer Simulation Edetic Acid/*pharmacology Endoribonucleases/*chemistry/drug effects Escherichia coli/chemistry Ferrous Compounds/*pharmacology Magnesium/pharmacology Models, Bacterial/*chemistry/drug effects RNA, Catalytic/*chemistry/drug effects RNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation Protein Binding RNA, Non-U.S. Gov't Support, P.H.S., Transfer/chemistry/metabolism Ribonuclease P Support, U.S. Gov't, Unité ARN
@article{,
title = {Mapping in three dimensions of regions in a catalytic RNA protected from attack by an Fe(II)-EDTA reagent},
author = {E Westhof and D Wesolowski and S Altman},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8636995},
isbn = {8636995},
year = {1996},
date = {1996-01-01},
journal = {J Mol Biol},
volume = {258},
number = {4},
pages = {600-613},
abstract = {The accessibility of the ribose groups in the phosphodiester chain of M1 RNA, the catalytic subunit of ribonuclease P from Escherichia coli, has been probed with an Fe(II)-EDTA reagent when the RNA is alone in solution, when it is in a complex with a tRNA precursor substrate, and when it is in the holoenzyme complex with its cofactor, C5 protein. The regions found to be protected under these various conditions, as well as those previously identified in other chemical probing experiments, have been mapped on a three-dimensional working model of M1 RNA and are generally compatible with the previously proposed placement of the substrate on the enzyme and with previous data and inferences regarding the interactions of C5 protein with M1 RNA. On the basis of the accessibilities of the C(4') atoms, refinements have been introduced in the model to accommodate the Fe(II)-EDTA protection data. The protein cofactor makes contact with several helical regions of the catalytic RNA on the opposite side of the surface to which substrates bind.},
note = {0022-2836
Journal Article},
keywords = {Bacterial Proteins/chemistry/metabolism Base Sequence Coenzymes/*chemistry/drug effects Computer Simulation Edetic Acid/*pharmacology Endoribonucleases/*chemistry/drug effects Escherichia coli/chemistry Ferrous Compounds/*pharmacology Magnesium/pharmacology Models, Bacterial/*chemistry/drug effects RNA, Catalytic/*chemistry/drug effects RNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation Protein Binding RNA, Non-U.S. Gov't Support, P.H.S., Transfer/chemistry/metabolism Ribonuclease P Support, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Holmes C E, Abraham A T, Hecht S M, Florentz C, Giege R
Fe.bleomycin as a probe of RNA conformation Article de journal
Dans: Nucleic Acids Res, vol. 24, no. 17, p. 3399-3406, 1996, ISBN: 8811095, (0305-1048 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Asp/chemistry RNA, Binding Sites Bleomycin/*analogs & derivatives/chemistry Models, FLORENTZ, Fungal/*chemistry RNA, Messenger/chemistry RNA, Molecular *Molecular Probes *Nucleic Acid Conformation RNA Precursors/chemistry RNA, Non-U.S. Gov't Support, P.H.S., Phe/chemistry Support, Transfer, Transfer/*chemistry RNA, U.S. Gov't, Unité ARN
@article{,
title = {Fe.bleomycin as a probe of RNA conformation},
author = {C E Holmes and A T Abraham and S M Hecht and C Florentz and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8811095},
isbn = {8811095},
year = {1996},
date = {1996-01-01},
journal = {Nucleic Acids Res},
volume = {24},
number = {17},
pages = {3399-3406},
abstract = {Two crystallographically defined tRNAs, yeast tRNAAsp and tRNAPhe, were used as substrates for oxidative cleavage by Fe.bleomycin to facilitate definition at high resolution of the structural elements in RNAs conducive to bleomycin binding and cleavage. Yeast tRNAAsp underwent cleavage at G45 and U66; yeast tRNAPhe was cleaved at four sites, namely G19, A31, U52 and A66. Only two of these six sites involved oxidative cleavage of a 5'-G.Pyr-3' sequence, but three sites were at the junction between single- and double-stranded regions of the RNA, consistent with a binding model in which the bithiazole + C-terminal substituent of bleomycin bind to minor groove structures on the RNA. Also studied were four tRNA transcripts believed on the basis of biochemical and chemical mapping experiments to share structural elements in common with the mature tRNAs. Cleavage of these tRNAs by Fe.bleomycin gave patterns of cleavage very different from each other and than those of the mature tRNAs. This observation suggests strongly that Fe.bleomycin cannot be used for chemical mapping in the same fashion as more classical reagents, such as Pb2+ or dimethyl sulfate. However, the great sensitivity of Fe.bleomycin to changes in nucleic acid structure argues that those species which do show similar patterns of cleavage must be very close in structure.},
note = {0305-1048
Journal Article},
keywords = {Asp/chemistry RNA, Binding Sites Bleomycin/*analogs & derivatives/chemistry Models, FLORENTZ, Fungal/*chemistry RNA, Messenger/chemistry RNA, Molecular *Molecular Probes *Nucleic Acid Conformation RNA Precursors/chemistry RNA, Non-U.S. Gov't Support, P.H.S., Phe/chemistry Support, Transfer, Transfer/*chemistry RNA, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Arts E J, Ghosh M, Jacques P S, Ehresmann B, Grice S F Le
Restoration of tRNA3Lys-primed(-)-strand DNA synthesis to an HIV-1 reverse transcriptase mutant with extended tRNAs. Implications for retroviral replication Article de journal
Dans: J Biol Chem, vol. 271, no. 15, p. 9054-9061, 1996, ISBN: 8621554, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence DNA, Calf Thymus/metabolism Sequence Deletion Structure-Activity Relationship Support, Complementary/biosynthesis DNA, Lys/*chemistry RNA-Directed DNA Polymerase/genetics/*metabolism Recombinant Proteins Ribonuclease H, Non-U.S. Gov't Support, P.H.S., Transfer, U.S. Gov't, Unité ARN, Viral/*biosynthesis HIV-1 Reverse Transcriptase Hydrogen Bonding Molecular Sequence Data Nucleic Acid Conformation RNA
@article{,
title = {Restoration of tRNA3Lys-primed(-)-strand DNA synthesis to an HIV-1 reverse transcriptase mutant with extended tRNAs. Implications for retroviral replication},
author = {E J Arts and M Ghosh and P S Jacques and B Ehresmann and S F Le Grice},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8621554},
isbn = {8621554},
year = {1996},
date = {1996-01-01},
journal = {J Biol Chem},
volume = {271},
number = {15},
pages = {9054-9061},
abstract = {The mechanism for the initiation of reverse transcription in human immunodeficiency virus type 1 (HIV-1) was studied utilizing a unique reverse transcriptase (RT) mutant altered in its noncatalytic p51 subunit. This mutant (p66/p51Delta13) retains full DNA- and RNA-dependent DNA polymerase activity but has reduced affinity for tRNA3Lys, the cognate HIV primer. When the ability to support(-)-strand DNA synthesis on a viral RNA template was evaluated, this mutant initiated from an 18-nucleotide (nt) oligoribo- or oligodeoxyribonucleotide primer complementary to the primer binding site (pbs). However, it failed to do so from natural and synthetic versions of tRNA3Lys. tRNA-primed(-)-strand synthesis could, however, be rescued by substituting the 76-nt tRNA3Lys with 81- and 107-nt tRNA-DNA chimeras, i.e. tRNA3Lys extended by 5 and 31 deoxyribonucleotides complementary to the viral genome upstream of the pbs. These findings imply that through interactions involving its p51 subunit, RT may be required to disrupt additional tRNA-viral RNA duplexes outside the pbs to proceed into productive(-)-strand DNA synthesis. Alternatively, specific interactions between tRNA3Lys and HIV-1 RT may be necessary for efficient initiation of(-)-strand DNA synthesis.},
note = {0021-9258
Journal Article},
keywords = {Base Sequence DNA, Calf Thymus/metabolism Sequence Deletion Structure-Activity Relationship Support, Complementary/biosynthesis DNA, Lys/*chemistry RNA-Directed DNA Polymerase/genetics/*metabolism Recombinant Proteins Ribonuclease H, Non-U.S. Gov't Support, P.H.S., Transfer, U.S. Gov't, Unité ARN, Viral/*biosynthesis HIV-1 Reverse Transcriptase Hydrogen Bonding Molecular Sequence Data Nucleic Acid Conformation RNA},
pubstate = {published},
tppubtype = {article}
}
O'Connor M., Brunelli C. A., Firpo M. A., Gregory S. T., Lieberman K. R., Lodmell J. S., Moine H., Ryk D. I. Van, Dahlberg A. E.
Genetic probes of ribosomal RNA function Article de journal
Dans: Biochem Cell Biol, vol. 73, no. 11-12, p. 859-68, 1995, (0829-8211 Journal Article Review Review, Tutorial).
Résumé | BibTeX | Étiquettes: 16S/genetics, Acid, Base, Conformation, Data, Gov't, Messenger/genetics, Molecular, Mutation, Non-U.S., Nucleic, P.H.S., Probes, Ribosomal, Ribosomal/*genetics, RNA, Sequence, Support, Transfer/genetics, U.S.
@article{,
title = {Genetic probes of ribosomal RNA function},
author = { M. O'Connor and C. A. Brunelli and M. A. Firpo and S. T. Gregory and K. R. Lieberman and J. S. Lodmell and H. Moine and D. I. Van Ryk and A. E. Dahlberg},
year = {1995},
date = {1995-01-01},
journal = {Biochem Cell Biol},
volume = {73},
number = {11-12},
pages = {859-68},
abstract = {We have used a genetic approach to uncover the functional roles of rRNA in protein synthesis. Mutations were constructed in a cloned rrn operon by site-directed mutagenesis or isolated by genetic selections following random mutagenesis. We have identified mutations that affect each step in the process of translation. The data are consistent with the results of biochemical and phylogenetic analyses but, in addition, have provided novel information on regions of rRNA not previously investigated.},
note = {0829-8211
Journal Article
Review
Review, Tutorial},
keywords = {16S/genetics, Acid, Base, Conformation, Data, Gov't, Messenger/genetics, Molecular, Mutation, Non-U.S., Nucleic, P.H.S., Probes, Ribosomal, Ribosomal/*genetics, RNA, Sequence, Support, Transfer/genetics, U.S.},
pubstate = {published},
tppubtype = {article}
}
O'Connor M, Brunelli C A, Firpo M A, Gregory S T, Lieberman K R, Lodmell J S, Moine H, Ryk D I Van, Dahlberg A E
Genetic probes of ribosomal RNA function Article de journal
Dans: Biochem Cell Biol, vol. 73, no. 11-12, p. 859-868, 1995, ISBN: 8722001, (0829-8211 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: 16S/genetics RNA, Base Sequence Molecular Sequence Data Mutation Nucleic Acid Conformation RNA Probes RNA, Messenger/genetics RNA, Non-U.S. Gov't Support, P.H.S., Ribosomal, Ribosomal/*genetics RNA, Transfer/genetics Support, U.S. Gov't, Unité ARN
@article{,
title = {Genetic probes of ribosomal RNA function},
author = {M O'Connor and C A Brunelli and M A Firpo and S T Gregory and K R Lieberman and J S Lodmell and H Moine and D I Van Ryk and A E Dahlberg},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8722001},
isbn = {8722001},
year = {1995},
date = {1995-01-01},
journal = {Biochem Cell Biol},
volume = {73},
number = {11-12},
pages = {859-868},
abstract = {We have used a genetic approach to uncover the functional roles of rRNA in protein synthesis. Mutations were constructed in a cloned rrn operon by site-directed mutagenesis or isolated by genetic selections following random mutagenesis. We have identified mutations that affect each step in the process of translation. The data are consistent with the results of biochemical and phylogenetic analyses but, in addition, have provided novel information on regions of rRNA not previously investigated.},
note = {0829-8211
Journal Article
Review
Review, Tutorial},
keywords = {16S/genetics RNA, Base Sequence Molecular Sequence Data Mutation Nucleic Acid Conformation RNA Probes RNA, Messenger/genetics RNA, Non-U.S. Gov't Support, P.H.S., Ribosomal, Ribosomal/*genetics RNA, Transfer/genetics Support, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Moine H., Dahlberg A. E.
Mutations in helix 34 of Escherichia coli 16 S ribosomal RNA have multiple effects on ribosome function and synthesis Article de journal
Dans: J Mol Biol, vol. 243, no. 3, p. 402-12, 1994, (0022-2836 Journal Article).
Résumé | BibTeX | Étiquettes: *Mutation, *Nucleic, *Translation, &, 16S/*chemistry/genetics, Acid, Base, beta-Galactosidase/genetics, Codon, coli/*genetics/growth, Conformation, Data, development, Escherichia, Genetic, Gov't, Molecular, Non-U.S., P.H.S., Ribosomal, Ribosomes/*metabolism, RNA, Sequence, Support, Terminator, U.S.
@article{,
title = {Mutations in helix 34 of Escherichia coli 16 S ribosomal RNA have multiple effects on ribosome function and synthesis},
author = { H. Moine and A. E. Dahlberg},
year = {1994},
date = {1994-01-01},
journal = {J Mol Biol},
volume = {243},
number = {3},
pages = {402-12},
abstract = {Helix 34 of E. coli 16 S rRNA (1046 to 1067 and 1189 to 1211) has been proposed to participate directly in the termination of translation at UGA stop codons. We have constructed mutations in this helix in plasmid-encoded rDNA to explore the specific functional roles of the sequence UCAUCA (1199 to 1204) and a secondary structure also involving positions 1054 and 1057-1058. The rRNA mutations were analyzed for their effects on in vivo translational accuracy (stop codon readthrough and frameshifting) as well as growth rate, ribosome synthesis and incorporation into polysomes. Mutations at positions 1054, 1057, 1058, 1199 and 1200 had significant effects on translational accuracy, causing non-specific readthrough of all three stop codons as well as enhanced +1 and -1 frameshifting. Mutations at 1202 and 1203, however, had no effect. The incorporation of deleterious mutant subunits into 70 S ribosomes and polysomes was severely reduced and was associated with a slower growth rate and increased synthesis of host-encoded ribosomes. These data support the proposal that helix 34 is an essential component of the decoding center of the 30 S ribosomal subunit and is not restricted in function to UGA-codon specific termination.},
note = {0022-2836
Journal Article},
keywords = {*Mutation, *Nucleic, *Translation, &, 16S/*chemistry/genetics, Acid, Base, beta-Galactosidase/genetics, Codon, coli/*genetics/growth, Conformation, Data, development, Escherichia, Genetic, Gov't, Molecular, Non-U.S., P.H.S., Ribosomal, Ribosomes/*metabolism, RNA, Sequence, Support, Terminator, U.S.},
pubstate = {published},
tppubtype = {article}
}
Westhof E, Altman S
Three-dimensional working model of M1 RNA, the catalytic RNA subunit of ribonuclease P from Escherichia coli Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 91, no. 11, p. 5133-5137, 1994, ISBN: 7515186, (0027-8424 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Bacterial/*chemistry/metabolism RNA, Base Sequence Computer Graphics Computer Simulation Endoribonucleases/*chemistry/metabolism Escherichia coli/*enzymology Molecular Sequence Data *Nucleic Acid Conformation RNA, Catalytic/*chemistry/metabolism Ribonuclease P Substrate Specificity Support, Non-U.S. Gov't Support, P.H.S., U.S. Gov't, Unité ARN
@article{,
title = {Three-dimensional working model of M1 RNA, the catalytic RNA subunit of ribonuclease P from Escherichia coli},
author = {E Westhof and S Altman},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7515186},
isbn = {7515186},
year = {1994},
date = {1994-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {91},
number = {11},
pages = {5133-5137},
abstract = {A three-dimensional model of M1 RNA, the catalytic RNA subunit of RNase P from Escherichia coli, was constructed with the aid of a computer. The modeling process took into account data from chemical and enzymatic protection experiments, phylogenetic analysis, studies of the activities of mutants, and the kinetics of reactions catalyzed by the binding of substrate to M1 RNA. The model provides a plausible picture of the binding to M1 RNA of the tRNA domain of a precursor tRNA substrate. The scissile bond and adjacent segments of the aminoacyl acceptor stem of a precursor tRNA substrate can fit into a cleft that leads to the phylogenetically conserved, central part of the structure.},
note = {0027-8424
Journal Article},
keywords = {Bacterial/*chemistry/metabolism RNA, Base Sequence Computer Graphics Computer Simulation Endoribonucleases/*chemistry/metabolism Escherichia coli/*enzymology Molecular Sequence Data *Nucleic Acid Conformation RNA, Catalytic/*chemistry/metabolism Ribonuclease P Substrate Specificity Support, Non-U.S. Gov't Support, P.H.S., U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Frugier M, Soll D, Giege R, Florentz C
Identity switches between tRNAs aminoacylated by class I glutaminyl- and class II aspartyl-tRNA synthetases Article de journal
Dans: Biochemistry, vol. 33, no. 33, p. 9912-9921, 1994, ISBN: 8060999, (0006-2960 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Acylation Aspartate-tRNA Ligase/chemistry/*metabolism Base Sequence Crystallization Escherichia coli/*enzymology/genetics Glutamate-tRNA Ligase/chemistry/*metabolism Kinetics Molecular Sequence Data Molecular Structure Mutation Nucleic Acid Conformation RNA, Asp/chemistry/*metabolism RNA, ERIANI, FLORENTZ, FRUGIER, Gln/chemistry/*metabolism Saccharomyces cerevisiae/*enzymology/genetics Support, Non-U.S. Gov't Support, P.H.S., Transfer, U.S. Gov't, Unité ARN
@article{,
title = {Identity switches between tRNAs aminoacylated by class I glutaminyl- and class II aspartyl-tRNA synthetases},
author = {M Frugier and D Soll and R Giege and C Florentz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8060999},
isbn = {8060999},
year = {1994},
date = {1994-01-01},
journal = {Biochemistry},
volume = {33},
number = {33},
pages = {9912-9921},
abstract = {High-resolution X-ray structures for the tRNA/aminoacyl-tRNA synthetase complexes between Escherichia coli tRNAGln/GlnRS and yeast tRNAAsp/AspRS have been determined. Positive identity nucleotides that direct aminoacylation specificity have been defined in both cases; E. coli tRNAGln identity is governed by 10 elements scattered in the tRNA structure, while specific aminoacylation of yeast tRNAAsp is dependent on 5 positions. Both identity sets are partially overlapping and share 3 nucleotides. Interestingly, the two enzymes belong to two different classes described for aminoacyl-tRNA synthetases. The class I glutaminyl-tRNA synthetase and the class II aspartyl-tRNA synthetase recognize their cognate tRNA from opposite sides. Mutants derived from glutamine and aspartate tRNAs have been created by progressively introducing identity elements from one tRNA into the other one. Glutaminylation and aspartylation assays of the transplanted tRNAs show that identity nucleotides from a tRNA originally aminoacylated by a synthetase from one class are still recognized if they are presented to the enzyme in a structural framework corresponding to a tRNA aminoacylated by a synthetase belonging to the other class. The simple transplantation of the glutamine identity set into tRNAAsp is sufficient to obtain glutaminylatable tRNA, but additional subtle features seem to be important for the complete conversion of tRNAGln in an aspartylatable substrate. This study defines C38 in yeast tRNAAsp as a new identity nucleotide for aspartylation. We show also in this paper that, during the complex formation, aminoacyl-tRNA synthetases are at least partially responsible for conformational changes which involve structural constraints in tRNA molecules.},
note = {0006-2960
Journal Article},
keywords = {Acylation Aspartate-tRNA Ligase/chemistry/*metabolism Base Sequence Crystallization Escherichia coli/*enzymology/genetics Glutamate-tRNA Ligase/chemistry/*metabolism Kinetics Molecular Sequence Data Molecular Structure Mutation Nucleic Acid Conformation RNA, Asp/chemistry/*metabolism RNA, ERIANI, FLORENTZ, FRUGIER, Gln/chemistry/*metabolism Saccharomyces cerevisiae/*enzymology/genetics Support, Non-U.S. Gov't Support, P.H.S., Transfer, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Wohrl B M, Ehresmann B, Keith G, Grice S F Le
Nuclease footprinting of human immunodeficiency virus reverse transcriptase/tRNA(Lys-3) complexes Article de journal
Dans: J Biol Chem, vol. 268, no. 18, p. 13617-13624, 1993, ISBN: 7685766, (0021-9258 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Anticodon Base Sequence HIV-1/*enzymology HIV-1 Reverse Transcriptase Hydrolysis Molecular Sequence Data Nucleic Acid Conformation RNA, Double-Stranded/metabolism RNA, Lys/chemistry/*metabolism RNA-Directed DNA Polymerase/*metabolism Recombinant Proteins/metabolism Ribonuclease, Non-U.S. Gov't Support, P.H.S., Pancreatic/metabolism Support, Transfer, U.S. Gov't, Unité ARN
@article{,
title = {Nuclease footprinting of human immunodeficiency virus reverse transcriptase/tRNA(Lys-3) complexes},
author = {B M Wohrl and B Ehresmann and G Keith and S F Le Grice},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7685766},
isbn = {7685766},
year = {1993},
date = {1993-01-01},
journal = {J Biol Chem},
volume = {268},
number = {18},
pages = {13617-13624},
abstract = {Nuclease footprinting has been used to probe features of binary complexes of type 1 human immunodeficiency virus reverse transcriptase (HIV-1 RT) with both natural and synthetic preparations of its cognate replication primer, tRNA(Lys-3). In addition to heterodimeric RT (p66/p51), ribonucleoprotein complexes containing either the p66 or p51 subunit were analyzed. Footprinting experiments employed both structure- and sequence-specific nucleases. Our results indicate a similar mode of interaction for the three RT preparations tested, suggesting contact with each loop of the tRNA primer (D, anticodon, and T psi C), as well as minor perturbation of the anticodon stem. Although there is little evidence for extensive disruption of the 3'-acceptor stem. RNase A footprinting data with natural and synthetic tRNA suggests that potential base pairing between the T psi C and D loops is disrupted in the presence of RT.},
note = {0021-9258
Journal Article},
keywords = {Anticodon Base Sequence HIV-1/*enzymology HIV-1 Reverse Transcriptase Hydrolysis Molecular Sequence Data Nucleic Acid Conformation RNA, Double-Stranded/metabolism RNA, Lys/chemistry/*metabolism RNA-Directed DNA Polymerase/*metabolism Recombinant Proteins/metabolism Ribonuclease, Non-U.S. Gov't Support, P.H.S., Pancreatic/metabolism Support, Transfer, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Schimmel P, Giege R, Moras D, Yokoyama S
An operational RNA code for amino acids and possible relationship to genetic code Article de journal
Dans: Proc Natl Acad Sci U S A, vol. 90, no. 19, p. 8763-8768, 1993, ISBN: 7692438, (0027-8424 Journal Article Review Review, Tutorial).
Résumé | Liens | BibTeX | Étiquettes: *Amino Acid Sequence Amino Acids/*metabolism Amino Acyl-tRNA Ligases/metabolism Base Sequence Conserved Sequence Escherichia coli/enzymology/genetics *Genetic Code Nucleic Acid Conformation Oligoribonucleotides RNA/*genetics RNA, Non-U.S. Gov't Support, P.H.S., Transfer/*genetics/metabolism Support, U.S. Gov't, Unité ARN
@article{,
title = {An operational RNA code for amino acids and possible relationship to genetic code},
author = {P Schimmel and R Giege and D Moras and S Yokoyama},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7692438},
isbn = {7692438},
year = {1993},
date = {1993-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {90},
number = {19},
pages = {8763-8768},
abstract = {RNA helical oligonucleotides that recapitulate the acceptor stems of transfer RNAs, and that are devoid of the anticodon trinucleotides of the genetic code, are aminoacylated by aminoacyl tRNA synthetases. The specificity of aminoacylation is sequence dependent, and both specificity and efficiency are generally determined by only a few nucleotides proximal to the amino acid attachment site. This sequence/structure-dependent aminoacylation of RNA oligonucleotides constitutes an operational RNA code for amino acids. To a rough approximation, members of the two different classes of tRNA synthetases are, like tRNAs, organized into two major domains. The class-defining conserved domain containing the active site incorporates determinants for recognition of RNA mini-helix substrates. This domain may reflect the primordial synthetase, which was needed for expression of the operational RNA code. The second synthetase domain, which generally is less or not conserved, provides for interactions with the second domain of tRNA, which incorporates the anticodon. The emergence of the genetic from the operational RNA code could occur when the second domain of synthetases was added with the anticodon-containing domain of tRNAs.},
note = {0027-8424
Journal Article
Review
Review, Tutorial},
keywords = {*Amino Acid Sequence Amino Acids/*metabolism Amino Acyl-tRNA Ligases/metabolism Base Sequence Conserved Sequence Escherichia coli/enzymology/genetics *Genetic Code Nucleic Acid Conformation Oligoribonucleotides RNA/*genetics RNA, Non-U.S. Gov't Support, P.H.S., Transfer/*genetics/metabolism Support, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}