M3i

@article{,

title = {Does the HIV-1 primer activation signal interact with tRNA3(Lys) during the initiation of reverse transcription?},

author = {V Goldschmidt 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=12560480},

isbn = {12560480},

year  = {2003},

date = {2003-01-01},

journal = {Nucleic Acids Res},

volume = {31},

number = {3},

pages = {850-859},

abstract = {Reverse transcription of HIV-1 RNA is primed by a tRNA3(Lys) molecule bound at the primer binding site (PBS). Complex intermolecular interactions were proposed between tRNA3(Lys) and the RNA of the HIV-1 Mal isolate. Recently, an alternative interaction was proposed between the TPsiC stem of tRNA3(Lys) and a primer activation signal (PAS) of the Lai and Hxb2 RNAs, suggesting major structural variations in the reverse transcription complex of different HIV-1 strains. Here, we analyzed mutants of the Hxb2 RNA that prevent the interaction between the PAS and tRNA3(Lys) or/and a complementary sequence in the viral RNA. We compared the kinetics of reverse transcription of the wild type and mutant Hxb2 RNAs, using either tRNA3(Lys) or an 18mer oligoribonucleotide complementary to the PBS, which cannot interact with the PAS, as primers. We also used chemical probing to test the structure of the mutant and wild type RNAs, as well as the complex formed between the later RNA and tRNA3(Lys). These experiments, together with the analysis of long term replication data of mutant viruses obtained by C. Morrow and coworkers (Birmingham, USA) that use alternate tRNAs as primers, strongly suggest that the interaction between the Hxb2 PAS and tRNA3(Lys) does not exist. Instead, the effects of the vRNA mutations on reverse transcription seem to be linked to incorrect folding of the mutant RNAs.},

note = {1362-4962 

Journal Article},

keywords = {Amino Acyl/chemistry/*metabolism  RNA, Base Sequence  Binding Sites  DNA Primers  DNA, Genetic, MARQUET, Non-U.S. Gov't  *Transcription, Transfer, Unité ARN, Viral  HIV-1/*genetics  HIV-1 Reverse Transcriptase/*metabolism  Kinetics  Molecular Sequence Data  Mutation  Nucleic Acid Conformation  Oligoribonucleotides  RNA, Viral/biosynthesis  *Gene Expression Regulation, Viral/chemistry/genetics/metabolism  Support},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {A 5'-3' long-range interaction in Ty1 RNA controls its reverse transcription and retrotransposition},

author = {G Cristofari and C Bampi and M Wilhelm and F X Wilhelm and J L Darlix},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=12169639},

isbn = {12169639},

year  = {2002},

date = {2002-01-01},

journal = {EMBO J},

volume = {21},

number = {16},

pages = {4368-4379},

abstract = {LTR-retrotransposons are abundant components of all eukaryotic genomes and appear to be key players in their evolution. They share with retroviruses a reverse transcription step during their replication cycle. To better understand the replication of retrotransposons as well as their similarities to and differences from retroviruses, we set up an in vitro model system to examine minus-strand cDNA synthesis of the yeast Ty1 LTR-retrotransposon. Results show that the 5' and 3' ends of Ty1 genomic RNA interact through 14 nucleotide 5'-3' complementary sequences (CYC sequences). This 5'-3' base pairing results in an efficient initiation of reverse transcription in vitro. Transposition of a marked Ty1 element and Ty1 cDNA synthesis in yeast rely on the ability of the CYC sequences to base pair. This 5'-3' interaction is also supported by phylogenic analysis of all full-length Ty1 and Ty2 elements present in the Saccharomyces cerevisiae genome. These novel findings lead us to propose that circularization of the Ty1 genomic RNA controls initiation of reverse transcription and may limit reverse transcription of defective retroelements.},

note = {0261-4189 

Journal Article},

keywords = {Complementary/biosynthesis  *Gene Expression Regulation, DNA, Fungal  In Vitro  Nucleic Acid Conformation  Phylogeny  RNA, Fungal/chemistry/*metabolism  RNA, Genetic, Messenger/chemistry/*metabolism  Retroelements/*genetics  Saccharomyces cerevisiae/*genetics  Support, Non-U.S. Gov't  *Transcription, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {In vitro evidence for the interaction of tRNA(3)(Lys) with U3 during the first strand transfer of HIV-1 reverse transcription},

author = {F Brule and G Bec and G Keith and S F Le Grice and B P Roques and B Ehresmann and C Ehresmann and R Marquet},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=10606665},

isbn = {10606665},

year  = {2000},

date = {2000-01-01},

journal = {Nucleic Acids Res},

volume = {28},

number = {2},

pages = {634-640},

abstract = {Over the course of its evolution, HIV-1 has taken maximum advantage of its tRNA(3)(Lys)primer by utilizing it in several steps of reverse transcription. Here, we have identified a conserved nonanucleotide sequence in the U3 region of HIV-1 RNA that is complementary to the anticodon stem of tRNA(3)(Lys). In order to test its possible role in the first strand transfer reaction, we applied an assay using a donor RNA corresponding to the 5'-part and an acceptor RNA spanning the 3'-part of HIV-1 RNA. In addition, we constructed two acceptor RNAs in which the nonanucleotide sequence complementary to tRNA(3)(Lys)was either substituted (S) or deleted (Delta). We used either natural tRNA(3)(Lys)or an 18 nt DNA as primer and measured the efficiency of (-) strand strong stop DNA transfer in the presence of wild-type, S or Delta acceptor RNA. Mutations in U3 did not decrease the transfer efficiency when reverse transcription was primed with the 18mer DNA. However, they significantly reduced the strand transfer efficiency in the tRNA(3)(Lys)-primed reactions. This reduction was also observed in the presence of nucleocapsid protein. These results suggest that tRNA(3)(Lys)increases (-) strand strong stop transfer by interacting with the U3 region of the genomic RNA. Sequence comparisons suggest that such long range interactions also exist in other lentiviruses.},

note = {1362-4962 

Journal Article},

keywords = {Base Sequence  HIV-1 Reverse Transcriptase/*metabolism  Nucleic Acid Conformation  Polymerase Chain Reaction  RNA, Genetic, Lys/*metabolism  RNA, MARQUET, Non-U.S. Gov't  *Transcription, Transfer, Unité ARN, Viral/chemistry/*metabolism  Support},

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 = {Heterogeneous terminal structure of Ty1 and Ty3 reverse transcripts},

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

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9153316},

isbn = {9153316},

year  = {1997},

date = {1997-01-01},

journal = {Nucleic Acids Res},

volume = {25},

number = {11},

pages = {2161-2166},

abstract = {A specific terminal structure of preintegrative DNA is required for transposition of retroviruses and LTR-retrotransposons. We have used an anchored PCR technique to map the 3'ends of DNA intermediates synthesized inside yeast Ty1 and Ty3 retrotransposon virus-like particles. We find that, unlike retroviruses, Ty1 replicated DNA does not have two extra base pairs at its 3'ends. In contrast some Ty3 preintegrative DNA molecules have two extra nucleotides at the 3'end of upstream and downstream long terminal repeats. Moreover we find that some molecules of replicated Ty3 DNA have more than two extra nucleotides at the 3'end of the upstream LTR. This observation could be accounted for by imprecise RNAse H cutting of the PPT sequence. The site of Ty1 and Ty3 plus-strand strong-stop DNA termination was also examined. Our results confirm that the prominent Ty1 and Ty3 plus-strand strong-stop molecules harbor 12 tRNA templated bases but also show that some Ty1 and Ty3 plus-strand strong-stop DNA molecules harbor less tRNA templated bases. We propose that these less than full length plus-strand molecules could be active intermediates in Ty retrotransposon replication.},

note = {0305-1048 

Journal Article},

keywords = {Calf Thymus/metabolism  Support, DNA Replication  DNA, Fungal/*chemistry/metabolism  *Nucleic Acid Conformation  Nucleic Acid Hybridization  Plasmids/chemistry/genetics/metabolism  Polymerase Chain Reaction  RNA, Genetic, Non-U.S. Gov't  *Transcription, Transfer/chemistry  Retroelements/*genetics  Ribonuclease H, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Structure and aminoacylation capacities of tRNA transcripts containing deoxyribonucleotides},

author = {R Aphasizhev and A Théobald-Dietrich and D Kostyuk and S N Kochetkov and L Kisselev and R Giege and F Fasiolo},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9257648},

isbn = {9257648},

year  = {1997},

date = {1997-01-01},

journal = {RNA},

volume = {3},

number = {8},

pages = {893-904},

abstract = {The contribution of the ribose 2'-hydroxyls to RNA structure and function has been analyzed, but still remains controversial. In this work, we report the use of a mutant T7 RNA polymerase as a tool in RNA studies, applied to the aspartate and methionine tRNA aminoacylation systems from yeast. Our approach consists of determining the effect of substituting natural ribonucleotides by deoxyribonucleotides in RNA and, thereby, defining the subset of important 2'-hydroxyl groups. We show that deoxyribose-containing RNA can be folded in a global conformation similar to that of natural RNA. Melting curves of tRNAs, obtained by temperature-gradient gel electrophoresis, indicate that in deoxyribo-containing molecules, the thermal stability of the tertiary network drops down, whereas the stability of the secondary structure remains unaltered. Nuclease footprinting reveals a significant increase in the accessibility of both single- and double-stranded regions. As to the functionality of the deoxyribose-containing tRNAs, their in vitro aminoacylation efficiency indicates striking differential effects depending upon the nature of the substituted ribonucleotides. Strongest decrease in charging occurs for yeast initiator tRNA(Met) transcripts containing dG or dC residues and for yeast tRNA(Asp) transcripts with dU or dG. In the aspartate system, the decreased aminoacylation capacities can be correlated with the substitution of the ribose moieties of U11 and G27, disrupting two hydrogen bond contacts with the synthetase. Altogether, this suggests that specific 2'-hydroxyl groups in tRNAs can act as determinants specifying aminoacylation identity.},

note = {1355-8382 

Journal Article},

keywords = {Asp/chemistry/genetics/metabolism  RNA, Base Sequence  DNA-Directed RNA Polymerases/genetics/metabolism  Deoxyribonucleotides/chemistry/*metabolism  Models, Genetic, Met/chemistry/genetics/metabolism  Structure-Activity Relationship  Support, Molecular  Molecular Sequence Data  Mutation  Nucleic Acid Conformation  RNA, Non-U.S. Gov't  *Transcription, Transfer, Transfer/*chemistry/genetics/*metabolism  RNA, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Structural and functional evidence that initiation and elongation of HIV-1 reverse transcription are distinct processes},

author = {J M Lanchy and C Isel and C Ehresmann and R Marquet and B Ehresmann},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=9150889},

isbn = {9150889},

year  = {1996},

date = {1996-01-01},

journal = {Biochimie},

volume = {78},

number = {11-12},

pages = {1087-1096},

abstract = {Retroviral reverse transcription starts with the extension of a cellular tRNA primer bound near the 5' end of the viral genomic RNA at a site called the primer binding site (PBS). Formation of the HIV-1 initiation complex between tRNA3(Lys), viral RNA and reverse transcriptase probably occurs during encapsidation of these components. tRNA3(Lys) is thought to be selectively packaged by interaction with the reverse transcriptase domain of the Pr160Gag-Pol precursor protein, then annealed to the PBS of viral RNA with the help of the nucleocapsid protein. tRNA3(Lys) and HIV-1 viral RNA form a highly-structured complex, with extended interactions between the two molecules. Two different modes of reverse transcription have been distinguished: initiation, a tRNA3(Lys)-specific and distributive mode of polymerization corresponding to the addition of the first five nucleotides, followed by elongation, a non-specific and processive mode of DNA synthesis. These two modes are reminiscent of the initiation and elongation processes previously observed with DNA-dependent RNA polymerases.},

note = {0300-9084 

Journal Article 

Review 

Review, Tutorial},

keywords = {Amino Acyl/*biosynthesis/*chemistry  RNA, Base Sequence  Comparative Study  HIV-1/*genetics/*metabolism  HIV-1 Reverse Transcriptase/*metabolism  Human  Molecular Sequence Data  *Nucleic Acid Conformation  RNA, Genetic, MARQUET, Non-U.S. Gov't  *Transcription, Transfer, Unité ARN, Viral/biosynthesis/chemistry  Retroviridae/metabolism  Support},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Initiation of reverse transcription of HIV-1: secondary structure of the HIV-1 RNA/tRNA(3Lys) (template/primer)},

author = {C Isel and C Ehresmann and G Keith and B Ehresmann and R Marquet},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7707372},

isbn = {7707372},

year  = {1995},

date = {1995-01-01},

journal = {J Mol Biol},

volume = {247},

number = {2},

pages = {236-250},

abstract = {Reverse transcription of human immunodeficiency virus type-1 (HIV-1) genomic RNA is primed by tRNA(3Lys), whose 3' end 18 nucleotides are complementary to the viral primer binding site (PBS). We used chemical and enzymatic probes to test the conformation of the viral RNA and tRNA(3Lys), in their free form and in the HIV-1 RNA/tRNA(3Lys) binary complex. Extensive reactivity changes were observed in both molecules upon formation of the binary complex. In the viral RNA, reactivity changes occurred up to 69 nucleotides upstream and 72 nucleotides downstream of the PBS. A secondary structure model of the HIV-1 RNA/tRNA(3Lys) complex accounting for all probing data has been constructed. It reveals an unexpectedly complex and compact pseudoknot-like structure in which most of the anticodon loop, the 3' strand of the anticodon stem and the 5' part of the variable loop of tRNA(3Lys) interact with viral sequences 12 to 39 nucleotides upstream of the PBS. The core of the binary complex is a complex junction formed by two single-stranded sequences of tRNA(3Lys), an intramolecular viral helix, an intramolecular tRNA helix, and two intermolecular helices formed by the template/primer interaction. This junction probably highly constrains the tertiary structure of the HIV-1 RNA/tRNA(3Lys) complex. Compared to the structure of the free molecules, only the D arm of tRNA(3Lys) and a small viral stem-loop downstream of the PBS are unaffected in the binary complex. Sequence comparison reveals that the main characteristics of the binary complex model are conserved among all HIV-1 isolates.},

note = {0022-2836 

Journal Article},

keywords = {Base Sequence  Binding Sites  Conserved Sequence  HIV-1/*genetics  Models, Genetic, Lys/*genetics/metabolism  RNA, MARQUET, Molecular  Molecular Probes  Molecular Sequence Data  *Nucleic Acid Conformation  RNA, Non-U.S. Gov't  *Transcription, Transfer, Unité ARN, Viral/*genetics/metabolism  Structure-Activity Relationship  Support},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {The differential transcriptional activity of two amphibian U1 small-nuclear RNA genes correlates with structural differences in the proximal sequence element},

author = {S Murgo and A Krol and P Carbon},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1735429},

isbn = {1735429},

year  = {1992},

date = {1992-01-01},

journal = {Eur J Biochem},

volume = {203},

number = {3},

pages = {443-447},

abstract = {We previously analyzed the transcription of an axolotl U1 small-nuclear RNA (snRNA) gene (AmU1) by microinjection into Xenopus laevis oocytes. In such an assay, AmU1 showed a low template activity compared to that of an X. laevis U1 snRNA gene (XlU1B2). Swapping the proximal sequence element (PSE) with that of XlU1B2 was required for AmU1 to acquire a transcription level equal to that of XlU1B2. In the present work, we examine the functional importance of the nucleotides that are common or different in both PSEs with the aim of identifying which nucleotides within the Xenopus U1 PSE are critical for this enhancement of Ambystoma mexicanum U1 snRNA transcription. The PSE mutation analysis showed that the central, phylogenetically conserved C-58/C-57 doublet is absolutely required for U1 promoter activity. In the 3' portion of this element, a CGC to ATG change (positions -54/-52) which partially restores the XlU1B2 PSE sequence, enables the AmU1 gene to gain the same transcriptional activity as XlU1B2. Remarkably, in this clustered point mutation, the sole C-54 to A-54 change is sufficient to obtain this increased level. Therefore, the activity of the AmU1 gene in injected Xenopus oocytes is strongly affected by a single sequence difference between AmU1 and XlU1B2 PSEs. This finding underscores the crucial importance of the nucleotide identity at position -54 to the function of the Xenopus U1 PSE.},

note = {0014-2956 

Journal Article},

keywords = {Ambystoma  Animals  Base Sequence  Microinjections  Molecular Sequence Data  Mutagenesis, Genetic  Xenopus laevis, Non-U.S. Gov't  *Transcription, Nucleic Acid  Sequence Homology, Nucleic Acid  Support, Site-Directed  Phylogeny  RNA, Small Nuclear/*genetics  *Regulatory Sequences, Unité ARN},

pubstate = {published},

tppubtype = {article}

}