Publications
2009
Geissmann T, Chevalier C, Cros M J, Boisset S, Fechter P, Noirot C, Schrenzel J, Francois P, Vandenesch F, Gaspin C, Romby P
A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation Journal Article
In: Nucleic Acids Res, vol. 37, no. 21, pp. 7239-7257, 2009, ISBN: 19786493, (1362-4962 (Electronic) 0305-1048 (Linking) Journal Article Research Support, Non-U.S. Gov't).
Abstract | Links | BibTeX | Tags: Bacillus subtilis/genetics/metabolism Base Sequence Computational Biology Conserved Sequence Gene Expression Profiling *Gene Expression Regulation, Bacterial Molecular Sequence Data Proteomics RNA Stability RNA, Genetic, Messenger/metabolism RNA, ROMBY, Unité ARN, Untranslated/*chemistry/genetics/metabolism Staphylococcus aureus/*genetics Transcription
@article{,
title = {A search for small noncoding RNAs in Staphylococcus aureus reveals a conserved sequence motif for regulation},
author = {T Geissmann and C Chevalier and M J Cros and S Boisset and P Fechter and C Noirot and J Schrenzel and P Francois and F Vandenesch and C Gaspin and P Romby},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19786493},
isbn = {19786493},
year = {2009},
date = {2009-01-01},
journal = {Nucleic Acids Res},
volume = {37},
number = {21},
pages = {7239-7257},
abstract = {Bioinformatic analysis of the intergenic regions of Staphylococcus aureus predicted multiple regulatory regions. From this analysis, we characterized 11 novel noncoding RNAs (RsaA-K) that are expressed in several S. aureus strains under different experimental conditions. Many of them accumulate in the late-exponential phase of growth. All ncRNAs are stable and their expression is Hfq-independent. The transcription of several of them is regulated by the alternative sigma B factor (RsaA, D and F) while the expression of RsaE is agrA-dependent. Six of these ncRNAs are specific to S. aureus, four are conserved in other Staphylococci, and RsaE is also present in Bacillaceae. Transcriptomic and proteomic analysis indicated that RsaE regulates the synthesis of proteins involved in various metabolic pathways. Phylogenetic analysis combined with RNA structure probing, searches for RsaE-mRNA base pairing, and toeprinting assays indicate that a conserved and unpaired UCCC sequence motif of RsaE binds to target mRNAs and prevents the formation of the ribosomal initiation complex. This study unexpectedly shows that most of the novel ncRNAs carry the conserved C-rich motif, suggesting that they are members of a class of ncRNAs that target mRNAs by a shared mechanism.},
note = {1362-4962 (Electronic)
0305-1048 (Linking)
Journal Article
Research Support, Non-U.S. Gov't},
keywords = {Bacillus subtilis/genetics/metabolism Base Sequence Computational Biology Conserved Sequence Gene Expression Profiling *Gene Expression Regulation, Bacterial Molecular Sequence Data Proteomics RNA Stability RNA, Genetic, Messenger/metabolism RNA, ROMBY, Unité ARN, Untranslated/*chemistry/genetics/metabolism Staphylococcus aureus/*genetics Transcription},
pubstate = {published},
tppubtype = {article}
}
Frechin M, Duchene A M, Becker H D
Translating organellar glutamine codons: a case by case scenario? Journal Article
In: RNA Biol, vol. 6, no. 1, pp. 31-34, 2009, ISBN: 19106621, (1555-8584 (Electronic) Journal Article Research Support, Non-U.S. Gov't Review).
Abstract | Links | BibTeX | Tags: Biological Nitrogenous Group Transferases/metabolism Plants/metabolism RNA, KERN Amino Acyl-tRNA Synthetases/metabolism Animals Chloroplasts/metabolism Codon Cytosol/metabolism Glutamate-tRNA Ligase/metabolism Glutamine/*chemistry Mitochondria/metabolism Models, Messenger/metabolism RNA, Transfer/metabolism, Unité ARN
@article{,
title = {Translating organellar glutamine codons: a case by case scenario?},
author = {M Frechin and A M Duchene and H D Becker},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19106621},
isbn = {19106621},
year = {2009},
date = {2009-01-01},
journal = {RNA Biol},
volume = {6},
number = {1},
pages = {31-34},
abstract = {Aminoacyl-tRNAs are generally formed by direct attachment of an amino acid to tRNAs by aminoacyl-tRNA synthetases, but glutaminyl-tRNA (Q-tRNA) is an exception to this rule. Glutaminyl-tRNA(Gln) (Q-tRNA(Q)) is formed by this direct pathway in the eukaryotic cytosol and in a small subset of bacteria, but is formed by an indirect transamidation pathway in most bacteria and archaea. To date it is almost impossible to predict what pathway generates organellar Q-tRNA(Q) in a given eukaryote. All eukaryotic genomes sequenced so far, display a single glutaminyl-tRNA synthetase (QRS) gene which is at least responsible for the cytosolic QRS activity, as well as a gene coding for a mitochondrial ortholog of the essential GatB subunit of the tRNA-dependent amidotransferase (AdT). Indeed, QRS activity was found in protozoan mitochondria while AdT activity was characterized in plant organelles. The pathway for Q-tRNA(Q) synthesis in yeast and mammals mitochondria is still questionable.},
note = {1555-8584 (Electronic)
Journal Article
Research Support, Non-U.S. Gov't
Review},
keywords = {Biological Nitrogenous Group Transferases/metabolism Plants/metabolism RNA, KERN Amino Acyl-tRNA Synthetases/metabolism Animals Chloroplasts/metabolism Codon Cytosol/metabolism Glutamate-tRNA Ligase/metabolism Glutamine/*chemistry Mitochondria/metabolism Models, Messenger/metabolism RNA, Transfer/metabolism, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
2004
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 Journal Article
In: Mol Microbiol, vol. 52, no. 3, pp. 661-675, 2004, ISBN: 15101974, (0950-382x Journal Article).
Abstract | Links | BibTeX | Tags: 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}
}
Dubois D Y, Blaise M, Becker H D, Campanacci V, Keith G, Giege R, Cambillau C, Lapointe J, Kern D
An aminoacyl-tRNA synthetase-like protein encoded by the Escherichia coli yadB gene glutamylates specifically tRNAAsp Journal Article
In: Proc Natl Acad Sci U S A, vol. 101, no. 20, pp. 7530-7535, 2004, ISBN: 15096594, (0027-8424 Journal Article).
Abstract | Links | BibTeX | Tags: Asp/*metabolism Support, KERN GIEGE Amino Acyl-tRNA Ligases/chemistry/genetics/*metabolism Crystallography, Messenger/metabolism RNA, Non-U.S. Gov't, Tertiary RNA, Transfer, Unité ARN, X-Ray Escherichia coli/enzymology/genetics/*metabolism Escherichia coli Proteins/chemistry/genetics/*metabolism Glutamic Acid/*metabolism Peptide Elongation Factor 2/metabolism Phylogeny Protein Structure
@article{,
title = {An aminoacyl-tRNA synthetase-like protein encoded by the Escherichia coli yadB gene glutamylates specifically tRNAAsp},
author = {D Y Dubois and M Blaise and H D Becker and V Campanacci and G Keith and R Giege and C Cambillau and J Lapointe and D Kern},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15096594},
isbn = {15096594},
year = {2004},
date = {2004-01-01},
journal = {Proc Natl Acad Sci U S A},
volume = {101},
number = {20},
pages = {7530-7535},
abstract = {The product of the Escherichia coli yadB gene is homologous to the N-terminal part of bacterial glutamyl-tRNA synthetases (GluRSs), including the Rossmann fold with the acceptor-binding domain and the stem-contact fold. This GluRS-like protein, which lacks the anticodon-binding domain, does not use tRNA(Glu) as substrate in vitro nor in vivo, but aminoacylates tRNA(Asp) with glutamate. The yadB gene is expressed in wild-type E. coli as an operon with the dksA gene, which encodes a protein involved in the general stress response by means of its action at the translational level. The fate of the glutamylated tRNA(Asp) is not known, but its incapacity to bind elongation factor Tu suggests that it is not involved in ribosomal protein synthesis. Genes homologous to yadB are present only in bacteria, mostly in Proteobacteria. Sequence alignments and phylogenetic analyses show that the YadB proteins form a distinct monophyletic group related to the bacterial and organellar GluRSs (alpha-type GlxRSs superfamily) with ubiquitous function as suggested by the similar functional properties of the YadB homologue from Neisseria meningitidis.},
note = {0027-8424
Journal Article},
keywords = {Asp/*metabolism Support, KERN GIEGE Amino Acyl-tRNA Ligases/chemistry/genetics/*metabolism Crystallography, Messenger/metabolism RNA, Non-U.S. Gov't, Tertiary RNA, Transfer, Unité ARN, X-Ray Escherichia coli/enzymology/genetics/*metabolism Escherichia coli Proteins/chemistry/genetics/*metabolism Glutamic Acid/*metabolism Peptide Elongation Factor 2/metabolism Phylogeny Protein Structure},
pubstate = {published},
tppubtype = {article}
}
2003
Wilhelm F X, Wilhelm M, Gabriel A
Extension and cleavage of the polypurine tract plus-strand primer by Ty1 reverse transcriptase Journal Article
In: J Biol Chem, vol. 278, no. 48, pp. 47678-47684, 2003, ISBN: 14500728, (0021-9258 Journal Article).
Abstract | Links | BibTeX | Tags: Base Sequence DNA/chemistry DNA Primers DNA Replication Models, Calf Thymus/chemistry Support, Genetic, Genetic Molecular Sequence Data Purines/*chemistry RNA/chemistry RNA, Messenger/metabolism RNA, Non-U.S. Gov't Support, P.H.S. Templates, U.S. Gov't, Unité ARN, Viral RNA-Directed DNA Polymerase/*chemistry Recombinant Proteins/chemistry Retroelements/*genetics Ribonuclease H
@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},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=14500728},
isbn = {14500728},
year = {2003},
date = {2003-01-01},
journal = {J Biol Chem},
volume = {278},
number = {48},
pages = {47678-47684},
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 Sequence DNA/chemistry DNA Primers DNA Replication Models, Calf Thymus/chemistry Support, Genetic, Genetic Molecular Sequence Data Purines/*chemistry RNA/chemistry RNA, Messenger/metabolism RNA, Non-U.S. Gov't Support, P.H.S. Templates, U.S. Gov't, Unité ARN, Viral RNA-Directed DNA Polymerase/*chemistry Recombinant Proteins/chemistry Retroelements/*genetics Ribonuclease H},
pubstate = {published},
tppubtype = {article}
}
Ryckelynck M, Giege R, Frugier M
Yeast tRNA(Asp) charging accuracy is threatened by the N-terminal extension of aspartyl-tRNA synthetase Journal Article
In: J Biol Chem, vol. 278, no. 11, pp. 9683-9690, 2003, ISBN: 12486031, (0021-9258 Journal Article).
Abstract | Links | BibTeX | Tags: Amino Acid Motifs Aspartate-tRNA Ligase/*metabolism Aspartic Acid/chemistry Base Sequence Codon Escherichia coli/metabolism Kinetics Molecular Sequence Data Nucleic Acid Conformation Nucleic Acids/chemistry Protein Structure, Asp/*chemistry Support, FRUGIER, Messenger/metabolism RNA, Non-U.S. Gov't Yeasts/metabolism, Secondary Protein Structure, Tertiary RNA, Transfer, Unité ARN
@article{,
title = {Yeast tRNA(Asp) charging accuracy is threatened by the N-terminal extension of aspartyl-tRNA synthetase},
author = {M Ryckelynck and R Giege and M Frugier},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12486031},
isbn = {12486031},
year = {2003},
date = {2003-01-01},
journal = {J Biol Chem},
volume = {278},
number = {11},
pages = {9683-9690},
abstract = {This study evaluates the role of the N-terminal extension from yeast aspartyl-tRNA synthetase in tRNA aspartylation. The presence of an RNA-binding motif in this extension, conserved in eukaryotic class IIb aminoacyl-tRNA synthetases, provides nonspecific tRNA binding properties to this enzyme. Here, it is assumed that the additional contacts the 70 amino acid-long appendix of aspartyl-tRNA synthetase makes with tRNA could be important in expression of aspartate identity in yeast. Using in vitro transcripts mutated at identity positions, it is demonstrated that the extension grants better aminoacylation efficiency but reduced specificity to the synthetase, increasing considerably the risk of noncognate tRNA mischarging. Yeast tRNA(Glu(UUC)) and tRNA(Asn(GUU)) were identified as the most easily mischarged tRNA species. Both have a G at the discriminator position, and their anticodon differs only by one change from the GUC aspartate anticodon.},
note = {0021-9258
Journal Article},
keywords = {Amino Acid Motifs Aspartate-tRNA Ligase/*metabolism Aspartic Acid/chemistry Base Sequence Codon Escherichia coli/metabolism Kinetics Molecular Sequence Data Nucleic Acid Conformation Nucleic Acids/chemistry Protein Structure, Asp/*chemistry Support, FRUGIER, Messenger/metabolism RNA, Non-U.S. Gov't Yeasts/metabolism, Secondary Protein Structure, Tertiary RNA, Transfer, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Frugier M, Giege R
Yeast aspartyl-tRNA synthetase binds specifically its own mRNA Journal Article
In: J Mol Biol, vol. 331, no. 2, pp. 375-383, 2003, ISBN: 12888345, (0022-2836 Journal Article).
Abstract | Links | BibTeX | Tags: 5' Untranslated Regions Amino Acid Motifs Aspartate-tRNA Ligase/*chemistry/metabolism Binding, Competitive Blotting, Drug Gene Expression Regulation, Enzymologic Genes, FRUGIER, Fungal Kinetics Luminescent Proteins/metabolism Plasmids Protein Binding Protein Structure, Messenger/metabolism RNA, Non-U.S. Gov't, Tertiary RNA/metabolism RNA, Transfer/metabolism Saccharomyces cerevisiae/metabolism Support, Unité ARN, Western Dose-Response Relationship
@article{,
title = {Yeast aspartyl-tRNA synthetase binds specifically its own mRNA},
author = {M Frugier and R Giege},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12888345},
isbn = {12888345},
year = {2003},
date = {2003-01-01},
journal = {J Mol Biol},
volume = {331},
number = {2},
pages = {375-383},
abstract = {Dimeric class II aspartyl-tRNA synthetase (AspRS) from yeast has a modular architecture and includes an N-terminal appendix of 70 amino acid residues that protrudes from the anticodon-binding module. This extension, of predicted helical structure, is not essential for aminoacylation but contains an RNA-binding motif that promotes non-specific interactions with tRNAs. As shown here, this protein extension can also interact with the 5' end of the AspRS mRNA. In vitro, optimal binding occurs on an mRNA domain comprising part of the 87 nucleotide long 5'UTR and the sequence encoding the N-terminal appendix. At the protein side, only the appendix and the anticodon-binding module participate in the interaction between AspRS and the mRNA domain. Binding is specific, since only tRNA(Asp) can dissociate the complex. In vivo, AspRS also binds specifically this mRNA domain and in doing so triggers a reduced translation of a fused GFP mRNA. From that, a mechanism for the regulation of this eukaryotic aminoacyl-tRNA synthetase is proposed. Implications for aspartylation accuracy in yeast are given.},
note = {0022-2836
Journal Article},
keywords = {5' Untranslated Regions Amino Acid Motifs Aspartate-tRNA Ligase/*chemistry/metabolism Binding, Competitive Blotting, Drug Gene Expression Regulation, Enzymologic Genes, FRUGIER, Fungal Kinetics Luminescent Proteins/metabolism Plasmids Protein Binding Protein Structure, Messenger/metabolism RNA, Non-U.S. Gov't, Tertiary RNA/metabolism RNA, Transfer/metabolism Saccharomyces cerevisiae/metabolism Support, Unité ARN, Western Dose-Response Relationship},
pubstate = {published},
tppubtype = {article}
}
Caillet J, Nogueira T, Masquida B, Winter F, Graffe M, Dock-Bregeon A C, Torres-Larios A, Sankaranarayanan R, Westhof E, Ehresmann B, Ehresmann C, Romby P, Springer M
The modular structure of Escherichia coli threonyl-tRNA synthetase as both an enzyme and a regulator of gene expression Journal Article
In: Mol Microbiol, vol. 47, no. 4, pp. 961-974, 2003, ISBN: 12581352, (0950-382x Journal Article).
Abstract | Links | BibTeX | Tags: Amino Acyl/chemistry/metabolism Ribosomes/metabolism Support, Bacterial Genes, Bacterial Macromolecular Systems Models, Bacterial/chemistry/metabolism RNA, Binding Sites Binding, Competitive Escherichia coli/*enzymology/*genetics Evolution, Messenger/metabolism RNA, Molecular Gene Expression Regulation, Molecular Molecular Mimicry Molecular Structure Mutation Operator Regions (Genetics) Protein Structure, Non-U.S. Gov't Threonine-tRNA Ligase/*chemistry/genetics/*metabolism, ROMBY, Tertiary Protein Subunits RNA, Transfer, Unité ARN, WESTHOF
@article{,
title = {The modular structure of Escherichia coli threonyl-tRNA synthetase as both an enzyme and a regulator of gene expression},
author = {J Caillet and T Nogueira and B Masquida and F Winter and M Graffe and A C Dock-Bregeon and A Torres-Larios and R Sankaranarayanan and E Westhof and B Ehresmann and C Ehresmann and P Romby and M Springer},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12581352},
isbn = {12581352},
year = {2003},
date = {2003-01-01},
journal = {Mol Microbiol},
volume = {47},
number = {4},
pages = {961-974},
abstract = {In addition to its role in tRNA aminoacylation, Escherichia coli threonyl-tRNA synthetase is a regulatory protein which binds a site, called the operator, located in the leader of its own mRNA and inhibits translational initiation by competing with ribosome binding. This work shows that the two essential steps of regulation, operator recognition and inhibition of ribosome binding, are performed by different domains of the protein. The catalytic and the C-terminal domain of the protein are involved in binding the two anticodon arm-like structures in the operator whereas the N-terminal domain of the enzyme is responsible for the competition with the ribosome. This is the first demonstration of a modular structure for a translational repressor and is reminiscent of that of transcriptional regulators. The mimicry between the operator and tRNA, suspected on the basis of previous experiments, is further supported by the fact that identical regions of the synthetase recognize both the operator and the tRNA anticodon arm. Based on these results, and recent structural data, we have constructed a computer-derived molecular model for the operator-threonyl-tRNA synthetase complex, which sheds light on several essential aspects of the regulatory mechanism.},
note = {0950-382x
Journal Article},
keywords = {Amino Acyl/chemistry/metabolism Ribosomes/metabolism Support, Bacterial Genes, Bacterial Macromolecular Systems Models, Bacterial/chemistry/metabolism RNA, Binding Sites Binding, Competitive Escherichia coli/*enzymology/*genetics Evolution, Messenger/metabolism RNA, Molecular Gene Expression Regulation, Molecular Molecular Mimicry Molecular Structure Mutation Operator Regions (Genetics) Protein Structure, Non-U.S. Gov't Threonine-tRNA Ligase/*chemistry/genetics/*metabolism, ROMBY, Tertiary Protein Subunits RNA, Transfer, Unité ARN, WESTHOF},
pubstate = {published},
tppubtype = {article}
}
2002
Lescure A, Fagegaltier D, Carbon P, Krol A
Protein factors mediating selenoprotein synthesis Journal Article
In: Curr Protein Pept Sci, vol. 3, no. 1, pp. 143-151, 2002, ISBN: 12370018, (1389-2037 Journal Article Review Review, Tutorial).
Abstract | Links | BibTeX | Tags: Bacterial Proteins/genetics/*metabolism Guanosine Triphosphate/metabolism Models, Biological Peptide Elongation Factors/*metabolism Protein Binding Proteins/*biosynthesis RNA, LESCURE, Messenger/metabolism RNA, Transfer/metabolism RNA-Binding Proteins/*metabolism, Unité ARN
@article{,
title = {Protein factors mediating selenoprotein synthesis},
author = {A Lescure and D Fagegaltier and P Carbon and A Krol},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12370018},
isbn = {12370018},
year = {2002},
date = {2002-01-01},
journal = {Curr Protein Pept Sci},
volume = {3},
number = {1},
pages = {143-151},
abstract = {The amino acid selenocysteine represents the major biological form of selenium. Both the synthesis of selenocysteine and its co-translational incorporation into selenoproteins in response to an in-frame UGA codon, require a complex molecular machinery. To decode the UGA Sec codon in eubacteria, this machinery comprises the tRNASec, the specialized elongation factor SelB and the SECIS hairpin in the selenoprotein mRNAs. SelB conveys the Sec-tRNASec to the A site of the ribosome through binding to the SECIS mRNA hairpin adjacent to the UGA Sec codon. SelB is thus a bifunctional factor, carrying functional homology to elongation factor EF-Tu in its N-terminal domain and SECIS RNA binding activity via its C-terminal extension. In archaea and eukaryotes, selenocysteine incorporation exhibits a higher degree of complexity because the SECIS hairpin is localized in the 3' untranslated region of the mRNA. In the last couple of years, remarkable progress has been made toward understanding the underlying mechanism in mammals. Indeed, the discovery of the SECIS RNA binding protein SBP2, which is not a translation factor, paved the way for the subsequent isolation of mSelB/EFSec, the mammalian homolog of SelB. In contrast to the eubacterial SelB, the specialized elongation factor mSelB/EFSec the SECIS RNA binding function. The role is carried out by SBP2 that also forms a protein-protein complex with mSelB/EFSec. As a consequence, an important difference between the eubacterial and eukaryal selenoprotein synthesis machineries is that the functions of SelB are divided into two proteins in eukaryotes. Obviously, selenoprotein synthesis represents a higher degree of complexity than anticipated, and more needs to be discovered in eukaryotes. In this review, we will focus on the structural and functional aspects of the SelB and SBP2 factors in selenoprotein synthesis.},
note = {1389-2037
Journal Article
Review
Review, Tutorial},
keywords = {Bacterial Proteins/genetics/*metabolism Guanosine Triphosphate/metabolism Models, Biological Peptide Elongation Factors/*metabolism Protein Binding Proteins/*biosynthesis RNA, LESCURE, Messenger/metabolism RNA, Transfer/metabolism RNA-Binding Proteins/*metabolism, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
2000
Kolb F A, Malmgren C, Westhof E, Ehresmann C, Ehresmann B, Wagner E G, Romby P
In: RNA, vol. 6, no. 3, pp. 311-324, 2000, ISBN: 10744017, (1355-8382 Journal Article).
Abstract | Links | BibTeX | Tags: Antisense/*metabolism RNA, Bacterial Proteins/*metabolism Base Pairing Base Sequence Binding Sites Cations, Divalent Computer Simulation Metals, Double-Stranded/metabolism RNA, Heavy/metabolism Models, Messenger/metabolism RNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA Stability RNA, Non-U.S. Gov't, ROMBY, Spliced Leader/metabolism Support, Unité ARN
@article{,
title = {An unusual structure formed by antisense-target RNA binding involves an extended kissing complex with a four-way junction and a side-by-side helical alignment},
author = {F A Kolb and C Malmgren and E Westhof and C Ehresmann and B Ehresmann and E G Wagner and P Romby},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10744017},
isbn = {10744017},
year = {2000},
date = {2000-01-01},
journal = {RNA},
volume = {6},
number = {3},
pages = {311-324},
abstract = {The antisense RNA CopA binds to the leader region of the repA mRNA (target: CopT). Previous studies on CopA-CopT pairing in vitro showed that the dominant product of antisense RNA-mRNA binding is not a full RNA duplex. We have studied here the structure of CopA-CopT complex, combining chemical and enzymatic probing and computer graphic modeling. CopI, a truncated derivative of CopA unable to bind CopT stably, was also analyzed. We show here that after initial loop-loop interaction (kissing), helix propagation resulted in an extended kissing complex that involves the formation of two intermolecular helices. By introducing mutations (base-pair inversions) into the upper stem regions of CopA and CopT, the boundaries of the two newly formed intermolecular helices were delimited. The resulting extended kissing complex represents a new type of four-way junction structure that adopts an asymmetrical X-shaped conformation formed by two helical domains, each one generated by coaxial stacking of two helices. This structure motif induces a side-by-side alignment of two long intramolecular helices that, in turn, facilitates the formation of an additional intermolecular helix that greatly stabilizes the inhibitory CopA-CopT RNA complex. This stabilizer helix cannot form in CopI-CopT complexes due to absence of the sequences involved. The functional significance of the three-dimensional models of the extended kissing complex (CopI-CopT) and the stable complex (CopA-CopT) are discussed.},
note = {1355-8382
Journal Article},
keywords = {Antisense/*metabolism RNA, Bacterial Proteins/*metabolism Base Pairing Base Sequence Binding Sites Cations, Divalent Computer Simulation Metals, Double-Stranded/metabolism RNA, Heavy/metabolism Models, Messenger/metabolism RNA, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA Stability RNA, Non-U.S. Gov't, ROMBY, Spliced Leader/metabolism Support, Unité ARN},
pubstate = {published},
tppubtype = {article}
}