Publications
2000
Lodmell J S, Ehresmann C, Ehresmann B, Marquet R
Convergence of natural and artificial evolution on an RNA loop-loop interaction: the HIV-1 dimerization initiation site Article de journal
Dans: RNA, vol. 6, no. 9, p. 1267-1276, 2000, ISBN: 10999604, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Codon, Initiator Dimerization Directed Molecular Evolution Evolution, MARQUET, Molecular HIV-1/*chemistry/genetics Nucleic Acid Conformation RNA, Non-U.S. Gov't, Unité ARN, Viral/*chemistry/metabolism Support
@article{,
title = {Convergence of natural and artificial evolution on an RNA loop-loop interaction: the HIV-1 dimerization initiation site},
author = {J S Lodmell 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=10999604},
isbn = {10999604},
year = {2000},
date = {2000-01-01},
journal = {RNA},
volume = {6},
number = {9},
pages = {1267-1276},
abstract = {Loop-loop interactions among nucleic acids constitute an important form of molecular recognition in a variety of biological systems. In HIV-1, genomic dimerization involves an intermolecular RNA loop-loop interaction at the dimerization initiation site (DIS), a hairpin located in the 5' noncoding region that contains an autocomplementary sequence in the loop. Only two major DIS loop sequence variants are observed among natural viral isolates. To investigate sequence and structural constraints on genomic RNA dimerization as well as loop-loop interactions in general, we randomized several or all of the nucleotides in the DIS loop and selected in vitro for dimerization-competent sequences. Surprisingly, increasing interloop complementarity above a threshold of 6 bp did not enhance dimerization, although the combinations of nucleotides forming the theoretically most stable hexanucleotide duplexes were selected. Noncanonical interactions contributed significantly to the stability and/or specificity of the dimeric complexes as demonstrated by the overwhelming bias for noncanonical base pairs closing the loop and covariations between flanking and central loop nucleotides. Degeneration of the entire loop yielded a complex population of dimerization-competent sequences whose consensus sequence resembles that of wild-type HIV-1. We conclude from these findings that the DIS has evolved to satisfy simultaneous constraints for optimal dimerization affinity and the capacity for homodimerization. Furthermore, the most constrained features of the DIS identified by our experiments could be the basis for the rational design of DIS-targeted antiviral compounds.},
note = {1355-8382
Journal Article},
keywords = {Codon, Initiator Dimerization Directed Molecular Evolution Evolution, MARQUET, Molecular HIV-1/*chemistry/genetics Nucleic Acid Conformation RNA, Non-U.S. Gov't, Unité ARN, Viral/*chemistry/metabolism Support},
pubstate = {published},
tppubtype = {article}
}
1999
Ennifar E, Yusupov M, Walter P, Marquet R, Ehresmann B, Ehresmann C, Dumas P
The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges Article de journal
Dans: Structure, vol. 7, no. 11, p. 1439-49, 1999, ISBN: 10574792, (0969-2126 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Adenine/*chemistry Base Pair Mismatch Base Sequence Crystallography, ENNIFAR, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't, Unité ARN, Viral/*chemistry/metabolism Support, X-Ray Dimerization HIV-1/*genetics Magnesium/metabolism Magnetic Resonance Spectroscopy Manganese/metabolism Models
@article{,
title = {The crystal structure of the dimerization initiation site of genomic HIV-1 RNA reveals an extended duplex with two adenine bulges},
author = {E Ennifar and M Yusupov and P Walter and R Marquet and B Ehresmann and C Ehresmann and P Dumas},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10574792},
isbn = {10574792},
year = {1999},
date = {1999-01-01},
journal = {Structure},
volume = {7},
number = {11},
pages = {1439-49},
abstract = {BACKGROUND: An important step in retroviral replication is dimerization of the genomic RNA prior to encapsidation. Dimerization is initiated by the formation of a transient 'kissing-loop complex' that is thought to be subsequently matured into an extended duplex by the nucleocapsid protein (NCp). Although chemical probing and nuclear magnetic resonance spectroscopy have provided insight into the structure of the kissing-loop structure, no structural information concerning the extended-duplex state is available so far. RESULTS: The structure of a minimal HIV-1 RNA dimerization initiation site has been solved at 2.3 A resolution in two different space groups. It reveals a 22 base pair extended duplex with two noncanonical Watson-Crick-like G-A mismatches, each adjacent to a bulged-out adenine. The structure shows significant asymmetry in deep groove width and G-A base-pair conformations. A network of eight magnesium cations was clearly identified, one being unusually chelated by the 3' phosphate of each bulge across an extremely narrowed deep major groove. CONCLUSIONS: These crystal structures represent the putative matured form of the initial kissing-loop complex. They show the ability of this self-complementary RNA hairpin loop to acquire a more stable extended duplex structure. Both bulged adenines form a striking 'base grip' that could be a recognition signal, either in cis for another viral RNA sequence, or in trans for a protein, possibly the NCp. Magnesium binding might be important to promote and stabilize the observed extrahelical conformation of these bulges.},
note = {0969-2126
Journal Article},
keywords = {Adenine/*chemistry Base Pair Mismatch Base Sequence Crystallography, ENNIFAR, Molecular Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't, Unité ARN, Viral/*chemistry/metabolism Support, X-Ray Dimerization HIV-1/*genetics Magnesium/metabolism Magnetic Resonance Spectroscopy Manganese/metabolism Models},
pubstate = {published},
tppubtype = {article}
}
1996
Felden B, Florentz C, Giege R, Westhof E
A central pseudoknotted three-way junction imposes tRNA-like mimicry and the orientation of three 5' upstream pseudoknots in the 3' terminus of tobacco mosaic virus RNA Article de journal
Dans: RNA, vol. 2, no. 3, p. 201-212, 1996, ISBN: 8608444, (1355-8382 Journal Article).
Résumé | Liens | BibTeX | Étiquettes: Base Sequence Computer Simulation Histidine-tRNA Ligase Models, FLORENTZ, Molecular Molecular Mimicry/*physiology Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't Tobacco Mosaic Virus/*chemistry, Transfer/chemistry RNA, Unité ARN, Viral/*chemistry/metabolism Support
@article{,
title = {A central pseudoknotted three-way junction imposes tRNA-like mimicry and the orientation of three 5' upstream pseudoknots in the 3' terminus of tobacco mosaic virus RNA},
author = {B Felden and C Florentz and R Giege and E Westhof},
url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8608444},
isbn = {8608444},
year = {1996},
date = {1996-01-01},
journal = {RNA},
volume = {2},
number = {3},
pages = {201-212},
abstract = {A three-dimensional model of the histidylable 3'-terminal tRNA-like domain of tobacco mosaic virus RNA is proposed on the basis of a comparative structural analysis, chemical and enzymatic probing, combined with graphical modeling of three RNA constructs of increasing size (38, 108, and 182 nt) derived from the 3'-terminal viral RNA sequence. The comparison between the probing patterns of the three RNAs allowed the determination of the relative orientation of these structural domains in the full-length viral tRNA-like structure. Modeling data indicate that only one of the two possible isomers of the three-way junction located at a central position of the tRNA-like domain is in agreement with structural data. Interestingly, this isomer gives rise to a molecule bearing a structural mimicry with the L-shape of canonical tRNAs. A pseudoknotted acceptor branch containing a T-like loop is located perpendicularly to an anticodon-like branch. Moreover, a single-stranded RNA stretch belonging to the pseudoknotted central core mimics a D-like loop and it is proposed that it interacts via two conserved guanosines with nucleotides of the T-like loop as found in canonical tRNAs. This model is valid for the 3' noncoding regions of tobamoviral RNAs as well as for the tRNA-like domain of the satellite tobacco mosaic virus RNA. All three molecules are substrates for yeast HisRS; however, whereas the complete viral genome is required for optimal histidylation capacities, both charging levels and affinity constants are decreased for the three RNA transcripts, suggesting that additional contacts located outside the tRNA-like domain are needed for an optimal aminoacylation process.},
note = {1355-8382
Journal Article},
keywords = {Base Sequence Computer Simulation Histidine-tRNA Ligase Models, FLORENTZ, Molecular Molecular Mimicry/*physiology Molecular Sequence Data *Nucleic Acid Conformation RNA, Non-U.S. Gov't Tobacco Mosaic Virus/*chemistry, Transfer/chemistry RNA, Unité ARN, Viral/*chemistry/metabolism Support},
pubstate = {published},
tppubtype = {article}
}