M3i

@article{,

title = {Pathology-related substitutions in human mitochondrial tRNA(Ile) reduce precursor 3' end processing efficiency in vitro},

author = {L Levinger and R Giege and C Florentz},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12655007},

isbn = {12655007},

year  = {2003},

date = {2003-01-01},

journal = {Nucleic Acids Res},

volume = {31},

number = {7},

pages = {1904-1912},

abstract = {The human mitochondrial genome encodes 22 tRNAs interspersed among the two rRNAs and 11 mRNAs, often without spacers, suggesting that tRNAs must be efficiently excised. Numerous maternally transmitted diseases and syndromes arise from mutations in mitochondrial tRNAs, likely due to defect(s) in tRNA metabolism. We have systematically explored the effect of pathogenic mutations on tRNA(Ile) precursor 3' end maturation in vitro by 3'-tRNase. Strikingly, four pathogenic tRNA(Ile) mutations reduce 3'-tRNase processing efficiency (V(max) / K(M)) to approximately 10-fold below that of wild-type, principally due to lower V(max). The structural impact of mutations was sought by secondary structure probing and wild-type tRNA(Ile) precursor was found to fold into a canonical cloverleaf. Among the mutant tRNA(Ile) precursors with the greatest 3' end processing deficiencies, only G4309A displays a secondary structure substantially different from wild-type, with changes in the T domain proximal to the substitution. Reduced efficiency of tRNA(Ile) precursor 3' end processing, in one case associated with structural perturbations, could thus contribute to human mitochondrial diseases caused by mutant tRNAs.},

note = {1362-4962 

Journal Article},

keywords = {Base Sequence  DNA, FLORENTZ, Ile/*genetics/metabolism  Support, Mitochondrial/*genetics  Endoribonucleases/metabolism  Hela Cells  Human  Kinetics  Molecular Sequence Data  Mutation  RNA Precursors/genetics/metabolism  *RNA Processing, Non-U.S. Gov't  Support, P.H.S., Post-Transcriptional  RNA, Transfer, U.S. Gov't, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Monitoring intermediate folding states of the td group I intron in vivo},

author = {C Waldsich and B Masquida and E Westhof and R Schroeder},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12356744},

isbn = {12356744},

year  = {2002},

date = {2002-01-01},

journal = {EMBO J},

volume = {21},

number = {19},

pages = {5281-5291},

abstract = {Group I introns consist of two major structural domains, the P4-P6 and P3-P9 domains, which assemble through interactions with peripheral extensions to fold into an active ribozyme. To assess group I intron folding in vivo, we probed the structure of td wild-type and mutant introns using dimethyl sulfate. The results suggest that the majority of the intron population is in the native state in accordance with the current structural model, which was refined to include two novel tertiary contacts. The importance of the loop E motif in the P7.1-P7.2 extension in assisting ribozyme folding was deduced from modeling and mutational analyses. Destabilization of stem P6 results in a deficiency in tertiary structure formation in both major domains, while weakening of stem P7 only interferes with folding of the P3-P9 domain. The different impact of mutations on the tertiary structure suggests that they interfere with folding at different stages. These results provide a first insight into the structure of folding intermediates and suggest a putative order of events in a hierarchical folding pathway in vivo.},

note = {0261-4189 

Journal Article},

keywords = {Bacterial/chemistry/genetics  Escherichia coli/genetics  Introns/*physiology  Models, Base Sequence  DNA, Molecular  Molecular Sequence Data  *Nucleic Acid Conformation  Support, Non-U.S. Gov't, Unité ARN, WESTHOF},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Secondary structure of the 3' terminus of hepatitis C virus minus-strand RNA},

author = {C Schuster and C Isel and I Imbert and C Ehresmann and R Marquet and M P Kieny},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12134011},

isbn = {12134011},

year  = {2002},

date = {2002-01-01},

journal = {J Virol},

volume = {76},

number = {16},

pages = {8058-8068},

abstract = {The 3'-terminal ends of both the positive and negative strands of the hepatitis C virus (HCV) RNA, the latter being the replicative intermediate, are most likely the initiation sites for replication by the viral RNA-dependent RNA polymerase, NS5B. The structural features of the very conserved 3' plus [(+)] strand untranslated region [3' (+) UTR] are well established (K. J. Blight and C. M. Rice, J. Virol. 71:7345-7352, 1997). However, little information is available concerning the 3' end of the minus [(-)] strand RNA. In the present work, we used chemical and enzymatic probing to investigate the conformation of that region, which is complementary to the 5' (+) UTR and the first 74 nucleotides of the HCV polyprotein coding sequence. By combining our experimental data with computer predictions, we have derived a secondary-structure model of this region. In our model, the last 220 nucleotides, where initiation of the (+) strand RNA synthesis presumably takes place, fold into five stable stem-loops, forming domain I. Domain I is linked to an overall less stable structure, named domain II, containing the sequences complementary to the pseudoknot of the internal ribosomal entry site in the 5' (+) UTR. Our results show that, even though the (-) strand 3'-terminal region has the antisense sequence of the 5' (+) UTR, it does not fold into its mirror image. Interestingly, comparison of the replication initiation sites on both strands reveals common structural features that may play key functions in the replication process.},

note = {0022-538x 

Journal Article},

keywords = {Base Sequence  DNA, MARQUET, Molecular  Molecular Probe Techniques  Molecular Sequence Data  Nucleic Acid Conformation  Plasmids/genetics  RNA, Non-U.S. Gov't  Virus Replication, Unité ARN, Viral/*chemistry/genetics  Support, Viral/genetics  Hepacivirus/*chemistry/genetics/physiology  Human  Models},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {NMR and biochemical characterization of recombinant human tRNA(Lys)3 expressed in Escherichia coli: identification of posttranscriptional nucleotide modifications required for efficient initiation of HIV-1 reverse transcription},

author = {C Tisne and M Rigourd and R Marquet and C Ehresmann and F Dardel},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=11073216},

isbn = {11073216},

year  = {2000},

date = {2000-01-01},

journal = {RNA},

volume = {6},

number = {10},

pages = {1403-1412},

abstract = {Reverse transcription of HIV-1 viral RNA uses human tRNA(Lys)3 as a primer. Some of the modified nucleotides carried by this tRNA must play a key role in the initiation of this process, because unmodified tRNA produced in vitro is only marginally active as primer. To provide a better understanding of the contribution of base modifications in the initiation complex, we have designed a recombinant system that allows tRNA(Lys)3 expression in Escherichia coli. Because of their high level of overexpression, some modifications are incorporated at substoichiometric levels. We have purified the two major recombinant tRNA(Lys)3 subspecies, and their modified nucleotide contents have been characterized by a combination of NMR and biochemical techniques. Both species carry psis, Ds, T, t6A, and m7G. Differences are observed at position 34, within the anticodon. One fraction lacks the 5-methylaminomethyl group, whereas the other lacks the 2-thio group. Although the s2U34-containing recombinant tRNA is a less efficient primer, it presents most of the characteristics of the mammalian tRNA. On the other hand, the mnm5U34-containing tRNA has a strongly reduced activity. Our results demonstrate that the modifications that are absent in E. coli (m2G10, psi27, m5C48, m5C49, and m1A58) as well as the mnm5 group at position 34 are dispensable for initiation of reverse transcription. In contrast, the 2-thio group at position 34 seems to play an important part in this process.},

note = {1355-8382 

Journal Article},

keywords = {Base Sequence  DNA, Biomolecular  *Nucleic Acid Conformation  RNA/*chemistry/genetics/metabolism  RNA, Genetic  Transcription, Genetic/*genetics  Virus Replication, Lys/*chemistry/genetics/metabolism  Structure-Activity Relationship  Support, MARQUET, Molecular  Molecular Sequence Data  Mutation/genetics  Nuclear Magnetic Resonance, Non-U.S. Gov't  Templates, Transfer, Unité ARN, Viral/biosynthesis/genetics  Escherichia coli/genetics  *Genetic Engineering  HIV-1/*genetics/physiology  Human  Iodine/metabolism  Models},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Reverse transcription of the yeast Ty1 retrotransposon: the mode of first strand transfer is either intermolecular or intramolecular},

author = {M Wilhelm and M Boutabout and T Heyman and F X Wilhelm},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10329158},

isbn = {10329158},

year  = {1999},

date = {1999-01-01},

journal = {J Mol Biol},

volume = {288},

number = {4},

pages = {505-510},

abstract = {Replication of the yeast Ty1 retrotransposon occurs by a mechanism similar to that of retroviruses. According to the current model of retroviral reverse transcription, two strand transfers (the so-called minus-strand and plus-strand strong-stop DNA transfers) are required to produce full-length preintegrative DNA. Because two genomic RNA molecules are packaged inside the viral particles, the strand transfers can be either intra- or intermolecular. To study the mode of transfer of minus-strand strong-stop DNA during reverse transcription of the yeast Ty1 retrotransposon, we have analyzed the cDNA products that accumulate in the cytoplasmic virus-like particles of yeast cells harboring two marked Ty1 elements. Our results indicate that Ty1 minus-strand transfer occurs in a random manner with approximately similar frequencies of intra- and intermolecular transfer. It has been observed recently that intra- and intermolecular minus-strand transfer occur at similar frequencies during replication of a complex retrovirus such as HIV-1. These results together with the observation that genetic recombination occurs with a high frequency during minus-strand synthesis suggest that both packaged RNA molecules are needed for the synthesis of one minus-strand DNA.},

note = {0022-2836 

Journal Article},

keywords = {Base Sequence  DNA, Genetic, Non-U.S. Gov't  *Transcription, Nucleic Acid  *Retroelements  Saccharomyces cerevisiae/*genetics  Support, Single-Stranded/genetics  Repetitive Sequences, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Primer selection by HIV-1 reverse transcriptase on RNA-tRNA(3Lys) and DNA-tRNA(3Lys) hybrids},

author = {G Yusupova and J M Lanchy and M Yusupov and G Keith and S F Le Grice and C Ehresmann and B Ehresmann and R Marquet},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8780773},

isbn = {8780773},

year  = {1996},

date = {1996-01-01},

journal = {J Mol Biol},

volume = {261},

number = {3},

pages = {315-321},

abstract = {During reverse transcription of the genomic RNA of human immunodeficiency virus type 1 (HIV-1) into double-stranded DNA, reverse transcriptase (RT) must accommodate RNA-RNA, DNA-RNA, RNA-DNA and DNA-DNA hybrids as primer-template. In this study, we examined extension of RNA-tRNA3Lys, and DNA-tRNA3Lys complexes by HIV-1 RT. When the 3' end of tRNA3Lys is annealed to oligoribonucleotides, tRNA3Lys, but not the complementary RNAs, is extended by HIV-1 RT, indicating that tRNA3Lys is efficiently used as primer and RNA as template. An opposite primer usage is observed when tRNA3Lys is annealed to complementary oligodeoxyribonucleotides. In this case, the oligodeoxyribonucleotides are efficiently used as primer and tRNA3Lys as template. This result indicates that the nature of nucleic acid bound to tRNA3Lys determines which strand of the RNA-tRNA3Lys and DNA-tRNA3Lys hybrids is extended by HIV-1 RT. When an oligoribonucleotide is annealed to an unmodified transcript of tRNA3Lys, both nucleic acids are extended by HIV-1 RT, indicating that specific selection of tRNA3Lys as primer requires the post-transcriptional modifications of tRNA3Lys.},

note = {0022-2836 

Journal Article},

keywords = {Base Sequence  DNA, Lys/genetics/*metabolism  RNA, MARQUET, Non-U.S. Gov't  Support, P.H.S., Post-Transcriptional  RNA, Transfer, U.S. Gov't, Unité ARN, Viral/genetics  HIV-1/*enzymology/genetics  HIV-1 Reverse Transcriptase  Human  Molecular Sequence Data  *RNA Processing, Viral/genetics  RNA-Directed DNA Polymerase/genetics/*metabolism  Support},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Restoration of tRNA3Lys-primed(-)-strand DNA synthesis to an HIV-1 reverse transcriptase mutant with extended tRNAs. Implications for retroviral replication},

author = {E J Arts and M Ghosh and P S Jacques and B Ehresmann and S F Le Grice},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8621554},

isbn = {8621554},

year  = {1996},

date = {1996-01-01},

journal = {J Biol Chem},

volume = {271},

number = {15},

pages = {9054-9061},

abstract = {The mechanism for the initiation of reverse transcription in human immunodeficiency virus type 1 (HIV-1) was studied utilizing a unique reverse transcriptase (RT) mutant altered in its noncatalytic p51 subunit. This mutant (p66/p51Delta13) retains full DNA- and RNA-dependent DNA polymerase activity but has reduced affinity for tRNA3Lys, the cognate HIV primer. When the ability to support(-)-strand DNA synthesis on a viral RNA template was evaluated, this mutant initiated from an 18-nucleotide (nt) oligoribo- or oligodeoxyribonucleotide primer complementary to the primer binding site (pbs). However, it failed to do so from natural and synthetic versions of tRNA3Lys. tRNA-primed(-)-strand synthesis could, however, be rescued by substituting the 76-nt tRNA3Lys with 81- and 107-nt tRNA-DNA chimeras, i.e. tRNA3Lys extended by 5 and 31 deoxyribonucleotides complementary to the viral genome upstream of the pbs. These findings imply that through interactions involving its p51 subunit, RT may be required to disrupt additional tRNA-viral RNA duplexes outside the pbs to proceed into productive(-)-strand DNA synthesis. Alternatively, specific interactions between tRNA3Lys and HIV-1 RT may be necessary for efficient initiation of(-)-strand DNA synthesis.},

note = {0021-9258 

Journal Article},

keywords = {Base Sequence  DNA, Calf Thymus/metabolism  Sequence Deletion  Structure-Activity Relationship  Support, Complementary/biosynthesis  DNA, Lys/*chemistry  RNA-Directed DNA Polymerase/genetics/*metabolism  Recombinant Proteins  Ribonuclease H, Non-U.S. Gov't  Support, P.H.S., Transfer, U.S. Gov't, Unité ARN, Viral/*biosynthesis  HIV-1 Reverse Transcriptase  Hydrogen Bonding  Molecular Sequence Data  Nucleic Acid Conformation  RNA},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {A three-dimensional model of hepatitis delta virus ribozyme based on biochemical and mutational analyses},

author = {N K Tanner and S Schaff and G Thill and E Petit-Koskas and A M Crain-Denoyelle and E Westhof},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7922369},

isbn = {7922369},

year  = {1994},

date = {1994-01-01},

journal = {Curr Biol},

volume = {4},

number = {6},

pages = {488-498},

abstract = {BACKGROUND: Hepatitis delta virus (HDV), which has a single-stranded RNA genome about 1700 nucleotides long, is a satellite virus of hepatitis B, and is associated with a high incidence of fulminant hepatitis and death in infected humans. Like certain pathogenic subviral RNAs that infect plants, HDV RNA features a closed-circular conformation, a rolling-circle mechanism of replication and RNA-catalyzed self-cleaving reactions of both genomic and anti-genomic strands in vitro. The catalytic domains cannot be folded into either the hammerhead or hairpin secondary-structure motifs that have been found in other self-cleaving RNAs. RESULTS: A pseudoknot secondary-structure model has been suggested for the catalytic domain (ribozyme) of HDV RNA. We conducted extensive mutational analyses of regions of the HDV ribozyme predicted in this model to be single stranded, and found that several of them are important for catalytic activity. We used these data, sequence comparisons between different isolates and previously published structural analyses to produce a computer graphic model of the three-dimensional architecture of the HDV ribozyme. CONCLUSIONS: Our model supports the pseudoknotted structure and rationalizes several observations relating to the lengths of the various stems and the sequence requirements of the single-stranded regions. It also provides insight into the catalytic mechanism of the HDV ribozyme. We specifically propose that residues C75, U20 and C21 form the basis of the catalytic region and are close to the cleavable phosphate.},

note = {0960-9822 

Journal Article},

keywords = {Base Sequence  DNA, Catalytic/*chemistry/genetics/metabolism  RNA, Molecular  Molecular Sequence Data  Mutagenesis, Non-U.S. Gov't, Nucleic Acid  Support, Site-Directed  Nucleic Acid Conformation  RNA, Unité ARN, Viral/chemistry/genetics/metabolism  Sequence Homology, Viral/genetics  Hepatitis Delta Virus/*enzymology/genetics  Human  Kinetics  Models},

pubstate = {published},

tppubtype = {article}

}