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2004
Burnouf D. Y., Olieric V., Wagner J., Fujii S., Reinbolt J., Fuchs R. P., Dumas P.
Structural and biochemical analysis of sliding clamp/ligand interactions suggest a competition between replicative and translesion DNA polymerases Journal Article
In: J Mol Biol, vol. 335, no. 5, pp. 1187-97, 2004, (0022-2836 Journal Article).
Abstract | BibTeX | Tags: *Binding, Antigen/metabolism, Bacterial/genetics, beta/*chemistry/genetics/*metabolism, Binding, Cell, coli/*enzymology, Competitive, Crystallization, DNA, DUMAS, Escherichia, Fragments/*metabolism, I/metabolism, III/metabolism, Kinetics, ligands, Models, Molecular, Nuclear, Peptide, Polymerase, Proliferating, Protein, Proteins/chemistry/metabolism, Recombinant, Replication/*genetics, Subunits
@article{,
title = {Structural and biochemical analysis of sliding clamp/ligand interactions suggest a competition between replicative and translesion DNA polymerases},
author = { D. Y. Burnouf and V. Olieric and J. Wagner and S. Fujii and J. Reinbolt and R. P. Fuchs and P. Dumas},
year = {2004},
date = {2004-01-01},
journal = {J Mol Biol},
volume = {335},
number = {5},
pages = {1187-97},
abstract = {Most DNA polymerases interact with their cognate processive replication factor through a small peptide, this interaction being absolutely required for their function in vivo. We have solved the crystal structure of a complex between the beta sliding clamp of Escherichia coli and the 16 residue C-terminal peptide of Pol IV (P16). The seven C-terminal residues bind to a pocket located at the surface of one beta monomer. This region was previously identified as the binding site of another beta clamp binding protein, the delta subunit of the gamma complex. We show that peptide P16 competitively prevents beta-clamp-mediated stimulation of both Pol IV and alpha subunit DNA polymerase activities, suggesting that the site of interaction of the alpha subunit with beta is identical with, or overlaps that of Pol IV. This common binding site for delta, Pol IV and alpha subunit is shown to be formed by residues that are highly conserved among many bacterial beta homologs, thus defining an evolutionarily conserved hydrophobic crevice for sliding clamp ligands and a new target for antibiotic drug design.},
note = {0022-2836
Journal Article},
keywords = {*Binding, Antigen/metabolism, Bacterial/genetics, beta/*chemistry/genetics/*metabolism, Binding, Cell, coli/*enzymology, Competitive, Crystallization, DNA, DUMAS, Escherichia, Fragments/*metabolism, I/metabolism, III/metabolism, Kinetics, ligands, Models, Molecular, Nuclear, Peptide, Polymerase, Proliferating, Protein, Proteins/chemistry/metabolism, Recombinant, Replication/*genetics, Subunits},
pubstate = {published},
tppubtype = {article}
}
Most DNA polymerases interact with their cognate processive replication factor through a small peptide, this interaction being absolutely required for their function in vivo. We have solved the crystal structure of a complex between the beta sliding clamp of Escherichia coli and the 16 residue C-terminal peptide of Pol IV (P16). The seven C-terminal residues bind to a pocket located at the surface of one beta monomer. This region was previously identified as the binding site of another beta clamp binding protein, the delta subunit of the gamma complex. We show that peptide P16 competitively prevents beta-clamp-mediated stimulation of both Pol IV and alpha subunit DNA polymerase activities, suggesting that the site of interaction of the alpha subunit with beta is identical with, or overlaps that of Pol IV. This common binding site for delta, Pol IV and alpha subunit is shown to be formed by residues that are highly conserved among many bacterial beta homologs, thus defining an evolutionarily conserved hydrophobic crevice for sliding clamp ligands and a new target for antibiotic drug design.
Grosjean H., Keith G., Droogmans L.
Detection and quantification of modified nucleotides in RNA using thin-layer chromatography Book Section
In: Gott, J. M. (Ed.): RNA Interference, Editing, and Modification: Methods and Protocols, vol. 265, pp. 357-91, Springer Protocols, Humana Press, 2004.
Abstract | BibTeX | Tags: &, 5', acids, and, Base, Chromatography, Composition, Deoxyribonucleotides/chemistry/isolation, DNA/chemistry/genetics/isolation, Endoribonucleases, Gov't, Indicators, Isotope, KEITH, Labeling/methods, Layer/methods, Non-U.S., Nucleic, Oligoribonucleotides/chemistry/isolation, Peptide, purification, Radioisotopes, Reagents, Regions/chemistry, Ribonucleotides/*analysis, RNA/*genetics/isolation, Support, Thin, Untranslated
@incollection{,
title = {Detection and quantification of modified nucleotides in RNA using thin-layer chromatography},
author = { H. Grosjean and G. Keith and L. Droogmans},
editor = { J.M. Gott},
year = {2004},
date = {2004-01-01},
booktitle = {RNA Interference, Editing, and Modification: Methods and Protocols},
volume = {265},
pages = {357-91},
publisher = {Springer Protocols, Humana Press},
series = {Methods in Molecular Biology},
abstract = {Identification of a modified nucleotide and its localization within an RNA molecule is a difficult task. Only direct sequencing of purified RNA molecules and high-performance liquid chromatography mass spectrometry analysis of purified RNA fragments allow determination of both the type and location of a given modified nucleotide within an RNA of 50-150 nt in length. The objective of this chapter is to describe in detail a few simple procedures that we have found particularly suited for the detection, localization, and quantification of modified nucleotides within an RNA of known sequence. The methods can also be used to reveal the enzymatic activity of a particular RNA-modifying enzyme in vitro or in vivo. The procedures are based on the use of radiolabeled RNA (with [32P], [14C], or [3H]) or [32P]-postlabeled oligonucleotides and two-dimensional thin-layer chromatography of labeled nucleotides on cellulose plates. This chapter provides useful maps of the migration characteristics of 70 modified nucleotides on thin-layer cellulose plates.},
keywords = {&, 5', acids, and, Base, Chromatography, Composition, Deoxyribonucleotides/chemistry/isolation, DNA/chemistry/genetics/isolation, Endoribonucleases, Gov't, Indicators, Isotope, KEITH, Labeling/methods, Layer/methods, Non-U.S., Nucleic, Oligoribonucleotides/chemistry/isolation, Peptide, purification, Radioisotopes, Reagents, Regions/chemistry, Ribonucleotides/*analysis, RNA/*genetics/isolation, Support, Thin, Untranslated},
pubstate = {published},
tppubtype = {incollection}
}
Identification of a modified nucleotide and its localization within an RNA molecule is a difficult task. Only direct sequencing of purified RNA molecules and high-performance liquid chromatography mass spectrometry analysis of purified RNA fragments allow determination of both the type and location of a given modified nucleotide within an RNA of 50-150 nt in length. The objective of this chapter is to describe in detail a few simple procedures that we have found particularly suited for the detection, localization, and quantification of modified nucleotides within an RNA of known sequence. The methods can also be used to reveal the enzymatic activity of a particular RNA-modifying enzyme in vitro or in vivo. The procedures are based on the use of radiolabeled RNA (with [32P], [14C], or [3H]) or [32P]-postlabeled oligonucleotides and two-dimensional thin-layer chromatography of labeled nucleotides on cellulose plates. This chapter provides useful maps of the migration characteristics of 70 modified nucleotides on thin-layer cellulose plates.
2003
Bonnal S., Schaeffer C., Creancier L., Clamens S., Moine H., Prats A. C., Vagner S.
A single internal ribosome entry site containing a G quartet RNA structure drives fibroblast growth factor 2 gene expression at four alternative translation initiation codons Journal Article
In: J Biol Chem, vol. 278, no. 41, pp. 39330-6, 2003, (0021-9258 Journal Article).
Abstract | BibTeX | Tags: 2/*genetics, Acid, Alternative, Base, Cell, Chain, Codon, Complementary/genetics, Conformation, Data, Deletion, DNA, Expression, Factor, Fibroblast, Gene, Gov't, Growth, Human, initiation, Initiator/genetics, Line, Messenger/*chemistry/*genetics, Molecular, Non-U.S., Nucleic, Peptide, Ribosomes/*metabolism, RNA, Sequence, Splicing, Support, Transfection
@article{,
title = {A single internal ribosome entry site containing a G quartet RNA structure drives fibroblast growth factor 2 gene expression at four alternative translation initiation codons},
author = { S. Bonnal and C. Schaeffer and L. Creancier and S. Clamens and H. Moine and A. C. Prats and S. Vagner},
year = {2003},
date = {2003-01-01},
journal = {J Biol Chem},
volume = {278},
number = {41},
pages = {39330-6},
abstract = {The 484-nucleotide (nt) alternatively translated region (ATR) of the human fibroblast growth factor 2 (FGF-2) mRNA contains four CUG and one AUG translation initiation codons. Although the 5'-end proximal CUG codon is initiated by a cap-dependent translation process, the other four initiation codons are initiated by a mechanism of internal entry of ribosomes. We undertook here a detailed analysis of the cis-acting elements defining the FGF-2 internal ribosome entry site (IRES). A thorough deletion analysis study within the 5'-ATR led us to define a 176-nt region as being necessary and sufficient for IRES function at four codons present in a downstream 308-nt RNA segment. Unexpectedly, a single IRES module is therefore responsible for translation initiation at four distantly localized codons. The determination of the FGF-2 5'-ATR RNA secondary structure by enzymatic and chemical probing experiments showed that the FGF-2 IRES contained two stem-loop regions and a G quartet motif that constitute novel structural determinants of IRES function.},
note = {0021-9258
Journal Article},
keywords = {2/*genetics, Acid, Alternative, Base, Cell, Chain, Codon, Complementary/genetics, Conformation, Data, Deletion, DNA, Expression, Factor, Fibroblast, Gene, Gov't, Growth, Human, initiation, Initiator/genetics, Line, Messenger/*chemistry/*genetics, Molecular, Non-U.S., Nucleic, Peptide, Ribosomes/*metabolism, RNA, Sequence, Splicing, Support, Transfection},
pubstate = {published},
tppubtype = {article}
}
The 484-nucleotide (nt) alternatively translated region (ATR) of the human fibroblast growth factor 2 (FGF-2) mRNA contains four CUG and one AUG translation initiation codons. Although the 5'-end proximal CUG codon is initiated by a cap-dependent translation process, the other four initiation codons are initiated by a mechanism of internal entry of ribosomes. We undertook here a detailed analysis of the cis-acting elements defining the FGF-2 internal ribosome entry site (IRES). A thorough deletion analysis study within the 5'-ATR led us to define a 176-nt region as being necessary and sufficient for IRES function at four codons present in a downstream 308-nt RNA segment. Unexpectedly, a single IRES module is therefore responsible for translation initiation at four distantly localized codons. The determination of the FGF-2 5'-ATR RNA secondary structure by enzymatic and chemical probing experiments showed that the FGF-2 IRES contained two stem-loop regions and a G quartet motif that constitute novel structural determinants of IRES function.
2002
Perederina A., Nevskaya N., Nikonov O., Nikulin A., Dumas P., Yao M., Tanaka I., Garber M., Gongadze G., Nikonov S.
Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex Journal Article
In: RNA, vol. 8, no. 12, pp. 1548-57, 2002, (1355-8382 Journal Article).
Abstract | BibTeX | Tags: 5S/*chemistry/*metabolism, Acid, Amino, Bacterial, Base, Binding, Bonding, coli/genetics, Conformation, Data, Escherichia, Fragments/chemistry/metabolism, Gov't, Hydrogen, Models, Molecular, Non-U.S., Nucleic, Peptide, Protein, Proteins/*chemistry/*metabolism, Proteins/chemistry/metabolism, Ribosomal, RNA, Sequence, Sites, Support
@article{,
title = {Detailed analysis of RNA-protein interactions within the bacterial ribosomal protein L5/5S rRNA complex},
author = { A. Perederina and N. Nevskaya and O. Nikonov and A. Nikulin and P. Dumas and M. Yao and I. Tanaka and M. Garber and G. Gongadze and S. Nikonov},
year = {2002},
date = {2002-01-01},
journal = {RNA},
volume = {8},
number = {12},
pages = {1548-57},
abstract = {The crystal structure of ribosomal protein L5 from Thermus thermophilus complexed with a 34-nt fragment comprising helix III and loop C of Escherichia coli 5S rRNA has been determined at 2.5 A resolution. The protein specifically interacts with the bulged nucleotides at the top of loop C of 5S rRNA. The rRNA and protein contact surfaces are strongly stabilized by intramolecular interactions. Charged and polar atoms forming the network of conserved intermolecular hydrogen bonds are located in two narrow planar parallel layers belonging to the protein and rRNA, respectively. The regions, including these atoms conserved in Bacteria and Archaea, can be considered an RNA-protein recognition module. Comparison of the T. thermophilus L5 structure in the RNA-bound form with the isolated Bacillus stearothermophilus L5 structure shows that the RNA-recognition module on the protein surface does not undergo significant changes upon RNA binding. In the crystal of the complex, the protein interacts with another RNA molecule in the asymmetric unit through the beta-sheet concave surface. This protein/RNA interface simulates the interaction of L5 with 23S rRNA observed in the Haloarcula marismortui 50S ribosomal subunit.},
note = {1355-8382
Journal Article},
keywords = {5S/*chemistry/*metabolism, Acid, Amino, Bacterial, Base, Binding, Bonding, coli/genetics, Conformation, Data, Escherichia, Fragments/chemistry/metabolism, Gov't, Hydrogen, Models, Molecular, Non-U.S., Nucleic, Peptide, Protein, Proteins/*chemistry/*metabolism, Proteins/chemistry/metabolism, Ribosomal, RNA, Sequence, Sites, Support},
pubstate = {published},
tppubtype = {article}
}
The crystal structure of ribosomal protein L5 from Thermus thermophilus complexed with a 34-nt fragment comprising helix III and loop C of Escherichia coli 5S rRNA has been determined at 2.5 A resolution. The protein specifically interacts with the bulged nucleotides at the top of loop C of 5S rRNA. The rRNA and protein contact surfaces are strongly stabilized by intramolecular interactions. Charged and polar atoms forming the network of conserved intermolecular hydrogen bonds are located in two narrow planar parallel layers belonging to the protein and rRNA, respectively. The regions, including these atoms conserved in Bacteria and Archaea, can be considered an RNA-protein recognition module. Comparison of the T. thermophilus L5 structure in the RNA-bound form with the isolated Bacillus stearothermophilus L5 structure shows that the RNA-recognition module on the protein surface does not undergo significant changes upon RNA binding. In the crystal of the complex, the protein interacts with another RNA molecule in the asymmetric unit through the beta-sheet concave surface. This protein/RNA interface simulates the interaction of L5 with 23S rRNA observed in the Haloarcula marismortui 50S ribosomal subunit.
