Publications
2004
Zhang H, Kolb F A, Jaskiewicz L, Westhof E, Filipowicz W
Single processing center models for human Dicer and bacterial RNase III Journal Article
In: Cell, vol. 118, no. 1, pp. 57-68, 2004, ISBN: 15242644, (0092-8674 Journal Article).
Abstract | Links | BibTeX | Tags: Amino Acid Support, Amino Acid Sequence Base Sequence Comparative Study Conserved Sequence Dimerization Endoribonucleases/*chemistry/genetics/isolation & purification/*metabolism Escherichia coli/enzymology Human Manganese/metabolism MicroRNAs/metabolism Models, Double-Stranded/chemistry/*metabolism RNA, Molecular Molecular Sequence Data Molecular Weight Mutagenesis, Non-U.S. Gov't, Post-Transcriptional RNA, Secondary Protein Structure, Site-Directed Mutation Protein Structure, Small Interfering/metabolism Recombinant Proteins/metabolism Ribonuclease III/*chemistry/genetics/isolation & purification/*metabolism Sequence Homology, Tertiary RNA Helicases/*chemistry/genetics/isolation & purification/*metabolism *RNA Processing, Unité ARN, WESTHOF
@article{,
title = {Single processing center models for human Dicer and bacterial RNase III},
author = {H Zhang and F A Kolb and L Jaskiewicz and E Westhof and W Filipowicz},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15242644},
isbn = {15242644},
year = {2004},
date = {2004-01-01},
journal = {Cell},
volume = {118},
number = {1},
pages = {57-68},
abstract = {Dicer is a multidomain ribonuclease that processes double-stranded RNAs (dsRNAs) to 21 nt small interfering RNAs (siRNAs) during RNA interference, and excises microRNAs from precursor hairpins. Dicer contains two domains related to the bacterial dsRNA-specific endonuclease, RNase III, which is known to function as a homodimer. Based on an X-ray structure of the Aquifex aeolicus RNase III, models of the enzyme interaction with dsRNA, and its cleavage at two composite catalytic centers, have been proposed. We have generated mutations in human Dicer and Escherichia coli RNase III residues implicated in the catalysis, and studied their effect on RNA processing. Our results indicate that both enzymes have only one processing center, containing two RNA cleavage sites and generating products with 2 nt 3' overhangs. Based on these and other data, we propose that Dicer functions through intramolecular dimerization of its two RNase III domains, assisted by the flanking RNA binding domains, PAZ and dsRBD.},
note = {0092-8674
Journal Article},
keywords = {Amino Acid Support, Amino Acid Sequence Base Sequence Comparative Study Conserved Sequence Dimerization Endoribonucleases/*chemistry/genetics/isolation & purification/*metabolism Escherichia coli/enzymology Human Manganese/metabolism MicroRNAs/metabolism Models, Double-Stranded/chemistry/*metabolism RNA, Molecular Molecular Sequence Data Molecular Weight Mutagenesis, Non-U.S. Gov't, Post-Transcriptional RNA, Secondary Protein Structure, Site-Directed Mutation Protein Structure, Small Interfering/metabolism Recombinant Proteins/metabolism Ribonuclease III/*chemistry/genetics/isolation & purification/*metabolism Sequence Homology, Tertiary RNA Helicases/*chemistry/genetics/isolation & purification/*metabolism *RNA Processing, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
Jaeger S, Eriani G, Martin F
Critical residues for RNA discrimination of the histone hairpin binding protein (HBP) investigated by the yeast three-hybrid system Journal Article
In: FEBS Lett, vol. 556, no. 1-3, pp. 265-270, 2004, ISBN: 14706861, (0014-5793 Journal Article).
Abstract | Links | BibTeX | Tags: Amino Acid Support, Amino Acid Sequence Amino Acid Substitution Base Sequence Carrier Proteins/chemistry/*genetics/*metabolism Histones/genetics Human Lac Operon/genetics Molecular Sequence Data Nucleic Acid Conformation Nucleotides/chemistry/genetics/metabolism RNA/chemistry/genetics/*metabolism RNA, ERIANI, Messenger/chemistry/genetics/metabolism RNA-Binding Proteins/chemistry/genetics/metabolism Recombinant Fusion Proteins/chemistry/genetics/metabolism Saccharomyces cerevisiae/*genetics Sequence Alignment Sequence Homology, Non-U.S. Gov't Two-Hybrid System Techniques beta-Galactosidase/genetics/metabolism, Unité ARN
@article{,
title = {Critical residues for RNA discrimination of the histone hairpin binding protein (HBP) investigated by the yeast three-hybrid system},
author = {S Jaeger and G Eriani and F Martin},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14706861},
isbn = {14706861},
year = {2004},
date = {2004-01-01},
journal = {FEBS Lett},
volume = {556},
number = {1-3},
pages = {265-270},
abstract = {The histone hairpin binding protein (HBP, also called SLBP, which stands for stem-loop binding protein) binds specifically to a highly conserved hairpin structure located in the 3' UTR of the cell-cycle-dependent histone mRNAs. HBP consists of a minimal central RNA binding domain (RBD) flanked by an N- and C-terminal domain. The yeast three-hybrid system has been used to investigate the critical residues of the human HBP involved in the binding of its target hairpin structure. By means of negative selections followed by positive selections, we isolated mutant HBP species. Our results indicate tight relationships between the RBD and the N- and C-terminal domains.},
note = {0014-5793
Journal Article},
keywords = {Amino Acid Support, Amino Acid Sequence Amino Acid Substitution Base Sequence Carrier Proteins/chemistry/*genetics/*metabolism Histones/genetics Human Lac Operon/genetics Molecular Sequence Data Nucleic Acid Conformation Nucleotides/chemistry/genetics/metabolism RNA/chemistry/genetics/*metabolism RNA, ERIANI, Messenger/chemistry/genetics/metabolism RNA-Binding Proteins/chemistry/genetics/metabolism Recombinant Fusion Proteins/chemistry/genetics/metabolism Saccharomyces cerevisiae/*genetics Sequence Alignment Sequence Homology, Non-U.S. Gov't Two-Hybrid System Techniques beta-Galactosidase/genetics/metabolism, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Campanacci V, Dubois D Y, Becker H D, Kern D, Spinelli S, Valencia C, Pagot F, Salomoni A, Grisel S, Vincentelli R, Bignon C, Lapointe J, Giege R, Cambillau C
The Escherichia coli YadB gene product reveals a novel aminoacyl-tRNA synthetase like activity Journal Article
In: J Mol Biol, vol. 337, no. 2, pp. 273-283, 2004, ISBN: 15003446, (0022-2836 Journal Article).
Abstract | Links | BibTeX | Tags: Amino Acid Support, Bacterial Glutamate-tRNA Ligase/chemistry/genetics/metabolism Glutamic Acid/metabolism Kinetics Ligands Models, Glu/metabolism Sequence Homology, KERN GIEGE Adenosine Monophosphate/metabolism Adenosine Triphosphate/metabolism Amino Acid Sequence Amino Acyl-tRNA Ligases/chemistry/*genetics/*metabolism Carrier Proteins/metabolism Crystallography, Molecular Molecular Sequence Data Neoplasm Proteins/metabolism Nuclear Proteins/metabolism Protein Conformation RNA, Non-U.S. Gov't Thermus thermophilus/enzymology/genetics Zinc/metabolism, Transfer, Unité ARN, X-Ray Escherichia coli/*enzymology/*genetics Escherichia coli Proteins/chemistry/*genetics/*metabolism Genes
@article{,
title = {The Escherichia coli YadB gene product reveals a novel aminoacyl-tRNA synthetase like activity},
author = {V Campanacci and D Y Dubois and H D Becker and D Kern and S Spinelli and C Valencia and F Pagot and A Salomoni and S Grisel and R Vincentelli and C Bignon and J Lapointe and R Giege and C Cambillau},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15003446},
isbn = {15003446},
year = {2004},
date = {2004-01-01},
journal = {J Mol Biol},
volume = {337},
number = {2},
pages = {273-283},
abstract = {In the course of a structural genomics program aiming at solving the structures of Escherichia coli open reading frame products of unknown function, we have determined the structure of YadB at 1.5A using molecular replacement. The YadB protein is 298 amino acid residues long and displays 34% sequence identity with E.coli glutamyl-tRNA synthetase (GluRS). It is much shorter than GluRS, which contains 468 residues, and lacks the complete domain interacting with the tRNA anticodon loop. As E.coli GluRS, YadB possesses a Zn2+ located in the putative tRNA acceptor stem-binding domain. The YadB cluster uses cysteine residues as the first three zinc ligands, but has a weaker tyrosine ligand at the fourth position. It shares with canonical amino acid RNA synthetases a major functional feature, namely activation of the amino acid (here glutamate). It differs, however, from GluRSs by the fact that the activation step is tRNA-independent and that it does not catalyze attachment of the activated glutamate to E.coli tRNAGlu, but to another, as yet unknown tRNA. These results suggest thus a novel function, distinct from that of GluRSs, for the yadB gene family.},
note = {0022-2836
Journal Article},
keywords = {Amino Acid Support, Bacterial Glutamate-tRNA Ligase/chemistry/genetics/metabolism Glutamic Acid/metabolism Kinetics Ligands Models, Glu/metabolism Sequence Homology, KERN GIEGE Adenosine Monophosphate/metabolism Adenosine Triphosphate/metabolism Amino Acid Sequence Amino Acyl-tRNA Ligases/chemistry/*genetics/*metabolism Carrier Proteins/metabolism Crystallography, Molecular Molecular Sequence Data Neoplasm Proteins/metabolism Nuclear Proteins/metabolism Protein Conformation RNA, Non-U.S. Gov't Thermus thermophilus/enzymology/genetics Zinc/metabolism, Transfer, Unité ARN, X-Ray Escherichia coli/*enzymology/*genetics Escherichia coli Proteins/chemistry/*genetics/*metabolism Genes},
pubstate = {published},
tppubtype = {article}
}
2003
Sauter C, Basquin J, Suck D
Sm-like proteins in Eubacteria: the crystal structure of the Hfq protein from Escherichia coli Journal Article
In: Nucleic Acids Res, vol. 31, no. 14, pp. 4091-4098, 2003, ISBN: 12853626, (1362-4962 Journal Article).
Abstract | Links | BibTeX | Tags: Amino Acid Support, Amino Acid Sequence Bacteria/*genetics Crystallography, FRUGIER, Molecular Host Factor 1 Protein/chemistry/*genetics Molecular Sequence Data Protein Conformation Protein Structure, Non-U.S. Gov't, SAUTER, Secondary Ribonucleoproteins, Small Nuclear/chemistry/*genetics Sequence Alignment Sequence Homology, Unité ARN, X-Ray Dimerization Escherichia coli Proteins/chemistry/*genetics Evolution
@article{,
title = {Sm-like proteins in Eubacteria: the crystal structure of the Hfq protein from Escherichia coli},
author = {C Sauter and J Basquin and D Suck},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12853626},
isbn = {12853626},
year = {2003},
date = {2003-01-01},
journal = {Nucleic Acids Res},
volume = {31},
number = {14},
pages = {4091-4098},
abstract = {The Hfq protein was discovered in Escherichia coli in the early seventies as a host factor for the Qbeta phage RNA replication. During the last decade, it was shown to be involved in many RNA processing events and remote sequence homology indicated a link to spliceosomal Sm proteins. We report the crystal structure of the E.coli Hfq protein showing that its monomer displays a characteristic Sm-fold and forms a homo-hexamer, in agreement with former biochemical data. Overall, the structure of the E.coli Hfq ring is similar to the one recently described for Staphylococcus aureus. This confirms that bacteria contain a hexameric Sm-like protein which is likely to be an ancient and less specialized form characterized by a relaxed RNA binding specificity. In addition, we identified an Hfq ortholog in the archaeon Methanococcus jannaschii which lacks a classical Sm/Lsm gene. Finally, a detailed structural comparison shows that the Sm-fold is remarkably well conserved in bacteria, Archaea and Eukarya, and represents a universal and modular building unit for oligomeric RNA binding proteins.},
note = {1362-4962
Journal Article},
keywords = {Amino Acid Support, Amino Acid Sequence Bacteria/*genetics Crystallography, FRUGIER, Molecular Host Factor 1 Protein/chemistry/*genetics Molecular Sequence Data Protein Conformation Protein Structure, Non-U.S. Gov't, SAUTER, Secondary Ribonucleoproteins, Small Nuclear/chemistry/*genetics Sequence Alignment Sequence Homology, Unité ARN, X-Ray Dimerization Escherichia coli Proteins/chemistry/*genetics Evolution},
pubstate = {published},
tppubtype = {article}
}
Charron C, Roy H, Blaise M, Giege R, Kern D
Non-discriminating and discriminating aspartyl-tRNA synthetases differ in the anticodon-binding domain Journal Article
In: EMBO J, vol. 22, no. 7, pp. 1632-1643, 2003, ISBN: 12660169, (0261-4189 Journal Article).
Abstract | Links | BibTeX | Tags: Amino Acid Support, Amino Acid Sequence *Anticodon Aspartate-tRNA Ligase/chemistry/*metabolism Binding Sites Models, Molecular Molecular Sequence Data Protein Conformation Pyrococcus/enzymology Sequence Homology, Non-U.S. Gov't Thermus thermophilus/enzymology, Unité ARN
@article{,
title = {Non-discriminating and discriminating aspartyl-tRNA synthetases differ in the anticodon-binding domain},
author = {C Charron and H Roy and M Blaise and R Giege and D Kern},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12660169},
isbn = {12660169},
year = {2003},
date = {2003-01-01},
journal = {EMBO J},
volume = {22},
number = {7},
pages = {1632-1643},
abstract = {In most organisms, tRNA aminoacylation is ensured by 20 aminoacyl-tRNA synthetases (aaRSs). In eubacteria, however, synthetases can be duplicated as in Thermus thermophilus, which contains two distinct AspRSs. While AspRS-1 is specific, AspRS-2 is non-discriminating and aspartylates tRNA(Asp) and tRNA(Asn). The structure at 2.3 A resolution of AspRS-2, the first of a non-discriminating synthetase, was solved. It differs from that of AspRS-1 but has resemblance to that of discriminating and archaeal AspRS from Pyrococcus kodakaraensis. The protein presents non-conventional features in its OB-fold anticodon-binding domain, namely the absence of a helix inserted between two beta-strands of this fold and a peculiar L1 loop differing from the large loops known to interact with tRNA(Asp) identity determinant C36 in conventional AspRSs. In AspRS-2, this loop is small and structurally homologous to that in AsnRSs, including conservation of a proline. In discriminating Pyrococcus AspRS, the L1 loop, although small, lacks this proline and is not superimposable with that of AspRS-2 or AsnRS. Its particular status is demonstrated by a loop-exchange experiment that renders the Pyrococcus AspRS non-discriminating.},
note = {0261-4189
Journal Article},
keywords = {Amino Acid Support, Amino Acid Sequence *Anticodon Aspartate-tRNA Ligase/chemistry/*metabolism Binding Sites Models, Molecular Molecular Sequence Data Protein Conformation Pyrococcus/enzymology Sequence Homology, Non-U.S. Gov't Thermus thermophilus/enzymology, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
2002
Lescure A, Allmang C, Yamada K, Carbon P, Krol A
cDNA cloning, expression pattern and RNA binding analysis of human selenocysteine insertion sequence (SECIS) binding protein 2 Journal Article
In: Gene, vol. 291, no. 1-2, pp. 279-285, 2002, ISBN: 12095701, (0378-1119 Journal Article).
Abstract | Links | BibTeX | Tags: Amino Acid Support, Amino Acid Sequence Blotting, Complementary/chemistry/genetics Female Gene Expression Human Male Molecular Sequence Data Peptide Elongation Factors/metabolism Protein Binding RNA/*metabolism RNA, DNA Sequence Homology, ERIANI, LESCURE, Messenger/genetics/metabolism RNA-Binding Proteins/genetics/*metabolism Sequence Alignment Sequence Analysis, Molecular DNA, Non-U.S. Gov't, Northern Cloning, Unité ARN
@article{,
title = {cDNA cloning, expression pattern and RNA binding analysis of human selenocysteine insertion sequence (SECIS) binding protein 2},
author = {A Lescure and C Allmang and K Yamada and P Carbon and A Krol},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12095701},
isbn = {12095701},
year = {2002},
date = {2002-01-01},
journal = {Gene},
volume = {291},
number = {1-2},
pages = {279-285},
abstract = {Selenocysteine and selenoprotein synthesis require a complex molecular machinery in mammals. Among the key players is the RNA-protein complex formed by the selenocysteine insertion sequence (SECIS) binding protein (SBP2) and the SECIS element, an RNA hairpin in the 3' untranslated regions of selenoprotein messenger RNAs (mRNAs). We have isolated the DNA complementary to mRNA of the human SBP2, enabling us to establish that it differs from a previously reported human SBP2-like protein. Examination of the expression pattern revealed that the human SBP2 protein is encoded by a 4 kb long mRNA that is over-expressed in testis. Compared to the rat SBP2 sequence, the human SBP2 protein displays two highly conserved domains with 92 and 95% amino acid identity, the latter one containing the RNA binding domain. The inter-domain section carries 55% sequence identity, the remainder of the SBP2 sequences showing about 65% identity, values lower than expected for two mammalian proteins. Interestingly, we could show that the binding of human SBP2 to the SECIS RNA is stimulated by the selenoprotein-specialized elongation translation factor mSelB/eEFsec.},
note = {0378-1119
Journal Article},
keywords = {Amino Acid Support, Amino Acid Sequence Blotting, Complementary/chemistry/genetics Female Gene Expression Human Male Molecular Sequence Data Peptide Elongation Factors/metabolism Protein Binding RNA/*metabolism RNA, DNA Sequence Homology, ERIANI, LESCURE, Messenger/genetics/metabolism RNA-Binding Proteins/genetics/*metabolism Sequence Alignment Sequence Analysis, Molecular DNA, Non-U.S. Gov't, Northern Cloning, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
2000
Wilhelm M, Boutabout M, Wilhelm F X
In: Biochem J, vol. 348, no. Pt 2, pp. 337-342, 2000, ISBN: 10816427, (0264-6021 Journal Article).
Abstract | Links | BibTeX | Tags: Affinity Cloning, Amino Acid Support, Amino Acid Sequence Chromatography, Calf Thymus/isolation & purification/*metabolism Saccharomyces cerevisiae/*enzymology/*genetics Sequence Alignment Sequence Homology, Genetic, Molecular Codon, Non-U.S. Gov't Templates, Unité ARN
@article{,
title = {Expression of an active form of recombinant Ty1 reverse transcriptase in Escherichia coli: a fusion protein containing the C-terminal region of the Ty1 integrase linked to the reverse transcriptase-RNase H domain exhibits polymerase and RNase H activities},
author = {M Wilhelm and M Boutabout and F X Wilhelm},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10816427},
isbn = {10816427},
year = {2000},
date = {2000-01-01},
journal = {Biochem J},
volume = {348},
number = {Pt 2},
pages = {337-342},
abstract = {Replication of the Saccharomyces cerevisiae Ty1 retrotransposon requires a reverse transcriptase capable of synthesizing Ty1 DNA. The first description of an active form of a recombinant Ty1 enzyme with polymerase and RNase H activities is reported here. The Ty1 enzyme was expressed as a hexahistidine-tagged fusion protein in Escherichia coli to facilitate purification of the recombinant protein by metal-chelate chromatography. Catalytic activity of the recombinant protein was detected only when amino acid residues encoded by the integrase gene were added to the N-terminus of the reverse transcriptase-RNase H domain. This suggests that the integrase domain could play a role in proper folding of reverse transcriptase. Several biochemical properties of the Ty1 enzyme were analysed, including the effect of MgCl(2), NaCl, temperature and of the chain terminator dideoxy GTP on its polymerase activity. RNase H activity was examined by monitoring the cleavage of a RNA-DNA template-primer. Our results suggest that the distance between the RNase H and polymerase active sites corresponds to the length of a 14-nucleotide RNA-DNA heteroduplex. The recombinant protein produced in E. coli should be useful for further biochemical and structural analyses and for a better understanding of the role of integrase in the activation of reverse transcriptase.},
note = {0264-6021
Journal Article},
keywords = {Affinity Cloning, Amino Acid Support, Amino Acid Sequence Chromatography, Calf Thymus/isolation & purification/*metabolism Saccharomyces cerevisiae/*enzymology/*genetics Sequence Alignment Sequence Homology, Genetic, Molecular Codon, Non-U.S. Gov't Templates, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Fagegaltier D, Hubert N, Yamada K, Mizutani T, Carbon P, Krol A
Characterization of mSelB, a novel mammalian elongation factor for selenoprotein translation Journal Article
In: EMBO J, vol. 19, no. 17, pp. 4796-4805, 2000, ISBN: 10970870, (0261-4189 Journal Article).
Abstract | Links | BibTeX | Tags: Amino Acid Support, Amino Acid Sequence Animals Bacterial Proteins/chemistry/*metabolism/physiology Caenorhabditis elegans/genetics Drosophila/genetics Hela Cells Human Mice Molecular Sequence Data Peptide Elongation Factors/chemistry/*metabolism/physiology Protein Binding Proteins/*genetics RNA, Amino Acyl/metabolism Sequence Homology, Genetic/*physiology, Non-U.S. Gov't Translation, Transfer, Unité ARN
@article{,
title = {Characterization of mSelB, a novel mammalian elongation factor for selenoprotein translation},
author = {D Fagegaltier and N Hubert and K Yamada and T Mizutani and P Carbon and A Krol},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10970870},
isbn = {10970870},
year = {2000},
date = {2000-01-01},
journal = {EMBO J},
volume = {19},
number = {17},
pages = {4796-4805},
abstract = {Decoding of UGA selenocysteine codons in eubacteria is mediated by the specialized elongation factor SelB, which conveys the charged tRNA(Sec) to the A site of the ribosome, through binding to the SECIS mRNA hairpin. In an attempt to isolate the eukaryotic homolog of SelB, a database search in this work identified a mouse expressed sequence tag containing the complete cDNA encoding a novel protein of 583 amino acids, which we called mSelB. Several lines of evidence enabled us to establish that mSelB is the bona fide mammalian elongation factor for selenoprotein translation: it binds GTP, recognizes the Sec-tRNA(Sec) in vitro and in vivo, and is required for efficient selenoprotein translation in vivo. In contrast to the eubacterial SelB, the recombinant mSelB alone is unable to bind specifically the eukaryotic SECIS RNA hairpin. However, complementation with HeLa cell extracts led to the formation of a SECIS-dependent complex containing mSelB and at least another factor. Therefore, the role carried out by a single elongation factor in eubacterial selenoprotein translation is devoted to two or more specialized proteins in eukaryotes.},
note = {0261-4189
Journal Article},
keywords = {Amino Acid Support, Amino Acid Sequence Animals Bacterial Proteins/chemistry/*metabolism/physiology Caenorhabditis elegans/genetics Drosophila/genetics Hela Cells Human Mice Molecular Sequence Data Peptide Elongation Factors/chemistry/*metabolism/physiology Protein Binding Proteins/*genetics RNA, Amino Acyl/metabolism Sequence Homology, Genetic/*physiology, Non-U.S. Gov't Translation, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Becker H D, Roy H, Moulinier L, Mazauric M H, Keith G, Kern D
Thermus thermophilus contains an eubacterial and an archaebacterial aspartyl-tRNA synthetase Journal Article
In: Biochemistry, vol. 39, no. 12, pp. 3216-3230, 2000, ISBN: 10727213, (0006-2960 Journal Article).
Abstract | Links | BibTeX | Tags: Amino Acid Support, Asn/genetics/metabolism RNA, Asp/metabolism Sequence Alignment Sequence Homology, Molecular Consensus Sequence Escherichia coli/enzymology/genetics Human Kinetics Molecular Sequence Data Peptide Fragments/chemistry RNA, Non-U.S. Gov't Support, P.H.S. Thermus thermophilus/*enzymology/genetics, Transfer, U.S. Gov't, Unité ARN
@article{,
title = {Thermus thermophilus contains an eubacterial and an archaebacterial aspartyl-tRNA synthetase},
author = {H D Becker and H Roy and L Moulinier and M H Mazauric and G Keith and D Kern},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10727213},
isbn = {10727213},
year = {2000},
date = {2000-01-01},
journal = {Biochemistry},
volume = {39},
number = {12},
pages = {3216-3230},
abstract = {Thermus thermophilus possesses two aspartyl-tRNA synthetases (AspRSs), AspRS1 and AspRS2, encoded by distinct genes. Alignment of the protein sequences with AspRSs of other origins reveals that AspRS1 possesses the structural features of eubacterial AspRSs, whereas AspRS2 is structurally related to the archaebacterial AspRSs. The structural dissimilarity between the two thermophilic AspRSs is correlated with functional divergences. AspRS1 aspartylates tRNA(Asp) whereas AspRS2 aspartylates tRNA(Asp), and tRNA(Asn) with similar efficiencies. Since Asp bound on tRNA(Asn) is converted into Asn by a tRNA-dependent aspartate amidotransferase, AspRS2 is involved in Asn-tRNA(Asn) formation. These properties relate functionally AspRS2 to archaebacterial AspRSs. The structural basis of the dual specificity of T. thermophilus tRNA(Asn) was investigated by comparing its sequence with those of tRNA(Asp) and tRNA(Asn) of strict specificity. It is shown that the thermophilic tRNA(Asn) contains the elements defining asparagine identity in Escherichia coli, part of which being also the major elements of aspartate identity, whereas minor elements of this identity are missing. The structural context that permits expression of aspartate and asparagine identities by tRNA(Asn) and how AspRS2 accommodates tRNA(Asp) and tRNA(Asn) will be discussed. This work establishes a distinct structure-function relationship of eubacterial and archaebacterial AspRSs. The structural and functional properties of the two thermophilic AspRSs will be discussed in the context of the modern and primitive pathways of tRNA aspartylation and asparaginylation and related to the phylogenetic connexion of T. thermophilus to eubacteria and archaebacteria.},
note = {0006-2960
Journal Article},
keywords = {Amino Acid Support, Asn/genetics/metabolism RNA, Asp/metabolism Sequence Alignment Sequence Homology, Molecular Consensus Sequence Escherichia coli/enzymology/genetics Human Kinetics Molecular Sequence Data Peptide Fragments/chemistry RNA, Non-U.S. Gov't Support, P.H.S. Thermus thermophilus/*enzymology/genetics, Transfer, U.S. Gov't, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
1999
Sankaranarayanan R, Dock-Bregeon A C, Romby P, Caillet J, Springer M, Rees B, Ehresmann C, Ehresmann B, Moras D
In: Cell, vol. 97, no. 3, pp. 371-381, 1999, ISBN: 10319817, (0092-8674 Journal Article).
Abstract | Links | BibTeX | Tags: Amino Acid Support, Amino Acyl/*chemistry/genetics/*metabolism Sequence Homology, Messenger/genetics RNA, Non-U.S. Gov't Zinc/*chemistry, ROMBY, Secondary Protein Structure, Tertiary RNA, Transfer, Unité ARN
@article{,
title = {The structure of threonyl-tRNA synthetase-tRNA(Thr) complex enlightens its repressor activity and reveals an essential zinc ion in the active site},
author = {R Sankaranarayanan and A C Dock-Bregeon and P Romby and J Caillet and M Springer and B Rees and C Ehresmann and B Ehresmann and D Moras},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10319817},
isbn = {10319817},
year = {1999},
date = {1999-01-01},
journal = {Cell},
volume = {97},
number = {3},
pages = {371-381},
abstract = {E. coli threonyl-tRNA synthetase (ThrRS) is a class II enzyme that represses the translation of its own mRNA. We report the crystal structure at 2.9 A resolution of the complex between tRNA(Thr) and ThrRS, whose structural features reveal novel strategies for providing specificity in tRNA selection. These include an amino-terminal domain containing a novel protein fold that makes minor groove contacts with the tRNA acceptor stem. The enzyme induces a large deformation of the anticodon loop, resulting in an interaction between two adjacent anticodon bases, which accounts for their prominent role in tRNA identity and translational regulation. A zinc ion found in the active site is implicated in amino acid recognition/discrimination.},
note = {0092-8674
Journal Article},
keywords = {Amino Acid Support, Amino Acyl/*chemistry/genetics/*metabolism Sequence Homology, Messenger/genetics RNA, Non-U.S. Gov't Zinc/*chemistry, ROMBY, Secondary Protein Structure, Tertiary RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
1997
Serganov A, Rak A, Garber M, Reinbolt J, Ehresmann B, Ehresmann C, Grunberg-Manago M, Portier C
Ribosomal protein S15 from Thermus thermophilus--cloning, sequencing, overexpression of the gene and RNA-binding properties of the protein Journal Article
In: Eur J Biochem, vol. 246, no. 2, pp. 291-300, 1997, ISBN: 9208917, (0014-2956 Journal Article).
Abstract | Links | BibTeX | Tags: 16S/metabolism RNA-Binding Proteins/*genetics/metabolism Ribosomal Proteins/*genetics/metabolism Sequence Homology, Amino Acid Support, Amino Acid Sequence Base Sequence Cloning, Bacterial Escherichia coli/genetics Molecular Sequence Data Plasmids RNA, Molecular DNA, Non-U.S. Gov't Thermus thermophilus/*genetics, Ribosomal, Unité ARN
@article{,
title = {Ribosomal protein S15 from Thermus thermophilus--cloning, sequencing, overexpression of the gene and RNA-binding properties of the protein},
author = {A Serganov and A Rak and M Garber and J Reinbolt and B Ehresmann and C Ehresmann and M Grunberg-Manago and C Portier},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9208917},
isbn = {9208917},
year = {1997},
date = {1997-01-01},
journal = {Eur J Biochem},
volume = {246},
number = {2},
pages = {291-300},
abstract = {A 6-kb DNA fragment from an extreme thermophile, Thermus thermophilus, carrying the genes for cytochrome oxidase ba3 subunit I (cbaA) and the ribosomal protein S15 (rpsO) was cloned into Escherichia coli. The gene rpsO was sequenced. The deduced amino acid sequence exhibits 59% identity to the corresponding protein from E. coli. Expression of rpsO in E. coli requires the use of a fully repressed inducible promoter because S15 from T. thermophilus is toxic for E. coli cells. When purified without denaturation from either overproducing E. coli strain or from T. thermophilus ribosomes, the S15 protein is stable and binds a cloned T. thermophilus 16S rRNA fragment (nucleotides 559-753), with low identical dissociation constants (2.5 nM), thus demonstrating that the thermophilic protein folds correctly in a mesophilic bacterium. The rRNA fragment bound corresponds in position and structure to the 16S rRNA fragment of E. coli. A similar high affinity was also found for the binding of S15 from T. thermophilus or E. coli to the corresponding E. coli 16S rRNA fragment, whereas a slightly lower affinity was observed in binding experiments between E. coli S15 and T. thermophilus 16S rRNA fragment. These results suggest that S15 from T. thermophilus recognizes similar determinants in both rRNA fragments. Competition experiments support this conclusion.},
note = {0014-2956
Journal Article},
keywords = {16S/metabolism RNA-Binding Proteins/*genetics/metabolism Ribosomal Proteins/*genetics/metabolism Sequence Homology, Amino Acid Support, Amino Acid Sequence Base Sequence Cloning, Bacterial Escherichia coli/genetics Molecular Sequence Data Plasmids RNA, Molecular DNA, Non-U.S. Gov't Thermus thermophilus/*genetics, Ribosomal, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
1996
Simos G, Segref A, Fasiolo F, Hellmuth K, Shevchenko A, Mann M, Hurt E C
The yeast protein Arc1p binds to tRNA and functions as a cofactor for the methionyl- and glutamyl-tRNA synthetases Journal Article
In: EMBO J, vol. 15, no. 19, pp. 5437-5448, 1996, ISBN: 8895587, (0261-4189 Journal Article).
Abstract | Links | BibTeX | Tags: Acylation Amino Acid Sequence Cytoplasm/chemistry Genes, Amino Acid Support, Fungal/genetics Glutamate-tRNA Ligase/*metabolism Kinetics Membrane Proteins/metabolism Methionine-tRNA Ligase/*metabolism Molecular Sequence Data Mutation Nuclear Envelope/metabolism RNA, Non-U.S. Gov't Yeasts/enzymology/*genetics/growth & development, Transfer/*metabolism RNA-Binding Proteins/analysis/genetics/*metabolism Recombinant Fusion Proteins/metabolism *Saccharomyces cerevisiae Proteins Sequence Homology, Unité ARN
@article{,
title = {The yeast protein Arc1p binds to tRNA and functions as a cofactor for the methionyl- and glutamyl-tRNA synthetases},
author = {G Simos and A Segref and F Fasiolo and K Hellmuth and A Shevchenko and M Mann and E C Hurt},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8895587},
isbn = {8895587},
year = {1996},
date = {1996-01-01},
journal = {EMBO J},
volume = {15},
number = {19},
pages = {5437-5448},
abstract = {Arc1p was found in a screen for components that interact genetically with Los1p, a nuclear pore-associated yeast protein involved in tRNA biogenesis. Arc1p is associated with two proteins which were identified as methionyl-tRNA and glutamyl-tRNA synthetase (MetRS and GluRS) by a new mass spectrometry method. ARC1 gene disruption leads to slow growth and reduced MetRS activity, and synthetically lethal arc1- mutants are complemented by the genes for MetRS and GluRS. Recombinant Arc1p binds in vitro to purified monomeric yeast MetRS, but not to an N-terminal truncated form, and strongly increases its apparent affinity for tRNAMet. Furthermore, Arc1p, which is allelic to the quadruplex nucleic acid binding protein G4p1, exhibits specific binding to tRNA as determined by gel retardation and UV-cross-linking. Arc1p is, therefore, a yeast protein with dual specificity: it associates with tRNA and aminoacyl-tRNA synthetases. This functional interaction may be required for efficient aminoacylation in vivo.},
note = {0261-4189
Journal Article},
keywords = {Acylation Amino Acid Sequence Cytoplasm/chemistry Genes, Amino Acid Support, Fungal/genetics Glutamate-tRNA Ligase/*metabolism Kinetics Membrane Proteins/metabolism Methionine-tRNA Ligase/*metabolism Molecular Sequence Data Mutation Nuclear Envelope/metabolism RNA, Non-U.S. Gov't Yeasts/enzymology/*genetics/growth & development, Transfer/*metabolism RNA-Binding Proteins/analysis/genetics/*metabolism Recombinant Fusion Proteins/metabolism *Saccharomyces cerevisiae Proteins Sequence Homology, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
1995
Schuster C, Myslinski E, Krol A, Carbon P
Staf, a novel zinc finger protein that activates the RNA polymerase III promoter of the selenocysteine tRNA gene Journal Article
In: EMBO J, vol. 14, no. 15, pp. 3777-3787, 1995, ISBN: 7641696, (0261-4189 Journal Article).
Abstract | Links | BibTeX | Tags: Amino Acid Support, Amino Acid Sequence Animals Base Sequence Cloning, Amino Acid-Specific/*genetics Recombinant Fusion Proteins/metabolism Sequence Analysis, DNA Sequence Homology, Messenger RNA, Molecular DNA/metabolism DNA-Binding Proteins/biosynthesis/genetics/*metabolism Gene Expression Genes, Non-U.S. Gov't Trans-Activation (Genetics)/*physiology Trans-Activators/biosynthesis/genetics/*metabolism Xenopus laevis *Zinc Fingers, Reporter Human Molecular Sequence Data Oocytes Promoter Regions (Genetics)/*genetics RNA Polymerase III/*genetics RNA, Transfer, Unité ARN
@article{,
title = {Staf, a novel zinc finger protein that activates the RNA polymerase III promoter of the selenocysteine tRNA gene},
author = {C Schuster and E Myslinski and A Krol and P Carbon},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7641696},
isbn = {7641696},
year = {1995},
date = {1995-01-01},
journal = {EMBO J},
volume = {14},
number = {15},
pages = {3777-3787},
abstract = {The selenocysteine tRNA gene (tRNA(Sec)) is atypical. Though transcribed by RNA polymerase III like all other tRNA genes, its basal promoter elements are distinct and reside essentially upstream of the coding region. In addition, transcription from the basal promoter is activated by a 15 bp activator element. In this report we describe the cloning and functional characterization of Staf (selenocysteine tRNA gene transcription activating factor), a novel Xenopus laevis transcription factor which binds to the tRNA(Sec) activator element and mediates its activation properties. The 600 amino acid Staf protein contains seven zinc fingers and a separate acidic activation domain. Seven highly conserved regions were detected between Staf and human ZNF76, a protein of unknown function, thereby aiding in predicting the locations of the functional domains of Staf. With the use of a novel expression assay in X.laevis oocytes we succeeded in demonstrating that Staf can activate the RNA polymerase III promoter of the tRNA(Sec) gene. This constitutes the first demonstration of the capacity of a cloned factor to activate RNA polymerase III transcription in vivo.},
note = {0261-4189
Journal Article},
keywords = {Amino Acid Support, Amino Acid Sequence Animals Base Sequence Cloning, Amino Acid-Specific/*genetics Recombinant Fusion Proteins/metabolism Sequence Analysis, DNA Sequence Homology, Messenger RNA, Molecular DNA/metabolism DNA-Binding Proteins/biosynthesis/genetics/*metabolism Gene Expression Genes, Non-U.S. Gov't Trans-Activation (Genetics)/*physiology Trans-Activators/biosynthesis/genetics/*metabolism Xenopus laevis *Zinc Fingers, Reporter Human Molecular Sequence Data Oocytes Promoter Regions (Genetics)/*genetics RNA Polymerase III/*genetics RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Logan D T, Mazauric M H, Kern D, Moras D
Crystal structure of glycyl-tRNA synthetase from Thermus thermophilus Journal Article
In: EMBO J, vol. 14, no. 17, pp. 4156-4167, 1995, ISBN: 7556056, (0261-4189 Journal Article).
Abstract | Links | BibTeX | Tags: Amino Acid Support, Amino Acid Sequence Binding Sites Comparative Study Crystallography, Bacterial Glycine-tRNA Ligase/*chemistry/genetics/isolation & purification Macromolecular Systems Models, Molecular Molecular Sequence Data Polymerase Chain Reaction *Protein Structure, Non-U.S. Gov't Thermus thermophilus/*enzymology, Secondary Sequence Homology, Unité ARN, X-Ray/methods DNA Probes Genes
@article{,
title = {Crystal structure of glycyl-tRNA synthetase from Thermus thermophilus},
author = {D T Logan and M H Mazauric and D Kern and D Moras},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7556056},
isbn = {7556056},
year = {1995},
date = {1995-01-01},
journal = {EMBO J},
volume = {14},
number = {17},
pages = {4156-4167},
abstract = {The sequence and crystal structure at 2.75 A resolution of the homodimeric glycyl-tRNA synthetase from Thermus thermophilus, the first representative of the last unknown class II synthetase subgroup, have been determined. The three class II synthetase sequence motifs are present but the structure was essential for identification of motif 1, which does not possess the proline previously believed to be an essential class II invariant. Nevertheless, crucial contacts with the active site of the other monomer involving motif 1 are conserved and a more comprehensive description of class II now becomes possible. Each monomer consists of an active site strongly resembling that of the aspartyl and seryl enzymes, a C-terminal anticodon recognition domain of 100 residues and a third domain unusually inserted between motifs 1 and 2 almost certainly interacting with the acceptor arm of tRNA(Gly). The C-terminal domain has a novel five-stranded parallel-antiparallel beta-sheet structure with three surrounding helices. The active site residues most probably responsible for substrate recognition, in particular in the Gly binding pocket, can be identified by inference from aspartyl-tRNA synthetase due to the conserved nature of the class II active site.},
note = {0261-4189
Journal Article},
keywords = {Amino Acid Support, Amino Acid Sequence Binding Sites Comparative Study Crystallography, Bacterial Glycine-tRNA Ligase/*chemistry/genetics/isolation & purification Macromolecular Systems Models, Molecular Molecular Sequence Data Polymerase Chain Reaction *Protein Structure, Non-U.S. Gov't Thermus thermophilus/*enzymology, Secondary Sequence Homology, Unité ARN, X-Ray/methods DNA Probes Genes},
pubstate = {published},
tppubtype = {article}
}
1993
Poterszman A, Plateau P, Moras D, Blanquet S, Mazauric M H, Kreutzer R, Kern D
In: FEBS Lett, vol. 325, no. 3, pp. 183-186, 1993, ISBN: 8319804, (0014-5793 Journal Article).
Abstract | Links | BibTeX | Tags: Amino Acid Support, Amino Acid Sequence Aspartate-tRNA Ligase/chemistry/*genetics/metabolism Base Sequence Cloning, Bacterial Models, Molecular Crystallization Genes, Molecular Molecular Sequence Data Oligodeoxyribonucleotides Sequence Homology, Non-U.S. Gov't Thermus thermophilus/*enzymology/genetics, Unité ARN
@article{,
title = {Sequence, overproduction and crystallization of aspartyl-tRNA synthetase from Thermus thermophilus. Implications for the structure of prokaryotic aspartyl-tRNA synthetases},
author = {A Poterszman and P Plateau and D Moras and S Blanquet and M H Mazauric and R Kreutzer and D Kern},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8319804},
isbn = {8319804},
year = {1993},
date = {1993-01-01},
journal = {FEBS Lett},
volume = {325},
number = {3},
pages = {183-186},
abstract = {The genes of aspartyl-tRNA synthetase (AspRS) from two Thermus thermophilus strain VK-1 and HB8, have been cloned and sequenced. Their nucleotidic sequences code for the same protein which displays the three characteristic motifs of class II aminoacyl-tRNA synthetases. This enzyme shows 50% identity with Escherichia coli AspRS, over the totality of the chain (580 amino acids). A comparison with the eukaryotic yeast cytoplasmic AspRS indicates the presence in the prokaryotic AspRS of an extra domain between motifs 2 and 3 much larger than in the eukaryotic ones. When its gene is under the control of the tac promoter of the expression vector pKK223-3, the protein is efficiently overexpressed as a thermostable protein in E. coli. It can be further purified to homogeneity using a heat treatment followed by a single anion exchange chromatography. Single crystals of the pure protein, diffracting at least to 2.2 A resolution (space group P2(1)2(1)2(1)},
note = {0014-5793
Journal Article},
keywords = {Amino Acid Support, Amino Acid Sequence Aspartate-tRNA Ligase/chemistry/*genetics/metabolism Base Sequence Cloning, Bacterial Models, Molecular Crystallization Genes, Molecular Molecular Sequence Data Oligodeoxyribonucleotides Sequence Homology, Non-U.S. Gov't Thermus thermophilus/*enzymology/genetics, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Oguiza J A, Malumbres M, Eriani G, Pisabarro A, Mateos L M, Martin F, Martin J F
In: J Bacteriol, vol. 175, no. 22, pp. 7356-7362, 1993, ISBN: 8226683, (0021-9193 Journal Article).
Abstract | Links | BibTeX | Tags: Amino Acid Support, Amino Acid Sequence Amino Acyl-tRNA Ligases/genetics Arginine/*pharmacology Arginine-tRNA Ligase/biosynthesis/*genetics Bacteria/enzymology Brevibacterium/*enzymology/*genetics Carboxy-Lyases/*genetics Cloning, Bacterial Molecular Sequence Data Molecular Weight *Multigene Family Plasmids Restriction Mapping Sequence Homology, Bacterial/*drug effects Gene Expression Regulation, Enzymologic/drug effects *Genes, ERIANI, Molecular Comparative Study Escherichia coli/genetics/growth & development Fungi/enzymology Gene Expression Regulation, Non-U.S. Gov't, Structural, Unité ARN
@article{,
title = {A gene encoding arginyl-tRNA synthetase is located in the upstream region of the lysA gene in Brevibacterium lactofermentum: regulation of argS-lysA cluster expression by arginine},
author = {J A Oguiza and M Malumbres and G Eriani and A Pisabarro and L M Mateos and F Martin and J F Martin},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8226683},
isbn = {8226683},
year = {1993},
date = {1993-01-01},
journal = {J Bacteriol},
volume = {175},
number = {22},
pages = {7356-7362},
abstract = {The Brevibacterium lactofermentum argS gene, which encodes an arginyl-tRNA synthetase, was identified in the upstream region of the lysA gene. The cloned gene was sequenced; it encodes a 550-amino-acid protein with an M(r) of 59,797. The deduced amino acid sequence showed 28% identical and 49% similar residues when compared with the sequence of the Escherichia coli arginyl-tRNA synthetase. The B. lactofermentum enzyme showed the highly conserved motifs of class I aminoacyl-tRNA synthetases. Expression of the argS gene in B. lactofermentum and E. coli resulted in an increase in aminoacyl-tRNA synthetase activity, correlated with the presence in sodium dodecyl sulfate-polyacrylamide gels of a clear protein band that corresponds to this enzyme. One single transcript of about 3,000 nucleotides and corresponding to the B. lactofermentum argS-lysA operon was identified. The transcription of these genes is repressed by lysine and induced by arginine, showing an interesting pattern of biosynthetic interlock between the pathways of both amino acids in corynebacteria.},
note = {0021-9193
Journal Article},
keywords = {Amino Acid Support, Amino Acid Sequence Amino Acyl-tRNA Ligases/genetics Arginine/*pharmacology Arginine-tRNA Ligase/biosynthesis/*genetics Bacteria/enzymology Brevibacterium/*enzymology/*genetics Carboxy-Lyases/*genetics Cloning, Bacterial Molecular Sequence Data Molecular Weight *Multigene Family Plasmids Restriction Mapping Sequence Homology, Bacterial/*drug effects Gene Expression Regulation, Enzymologic/drug effects *Genes, ERIANI, Molecular Comparative Study Escherichia coli/genetics/growth & development Fungi/enzymology Gene Expression Regulation, Non-U.S. Gov't, Structural, Unité ARN},
pubstate = {published},
tppubtype = {article}
}