Gilmer O, Quignon E, Jousset A C, Paillart J C, Marquet R, Vivet-Boudou V
Chemical and Enzymatic Probing of Viral RNAs: From Infancy to Maturity and Beyond Journal Article
In: Viruses, vol. 13, no. 10, pp. 1894, 2021.
Abstract | Links | BibTeX | Tags: Capillary electrophoresis, chemical probe, enzymatic probe, high-throughput sequencing, MARQUET, mutational profiling, PAILLART, RNA, SHAPE, structure, Unité ARN
@article{nokey,
title = {Chemical and Enzymatic Probing of Viral RNAs: From Infancy to Maturity and Beyond},
author = {O Gilmer and E Quignon and A C Jousset and J C Paillart and R Marquet and V Vivet-Boudou},
url = {https://www.mdpi.com/1999-4915/13/10/1894},
doi = {v13101894},
year = {2021},
date = {2021-01-01},
urldate = {2021-01-01},
journal = {Viruses},
volume = {13},
number = {10},
pages = {1894},
abstract = {RNA molecules are key players in a variety of biological events, and this is particularly true for viral RNAs. To better understand the replication of those pathogens and try to block them, special attention has been paid to the structure of their RNAs. Methods to probe RNA structures have been developed since the 1960s; even if they have evolved over the years, they are still in use today and provide useful information on the folding of RNA molecules, including viral RNAs. The aim of this review is to offer a historical perspective on the structural probing methods used to decipher RNA structures before the development of the selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) methodology and to show how they have influenced the current probing techniques. Actually, these technological breakthroughs, which involved advanced detection methods, were made possible thanks to the development of next-generation sequencing (NGS) but also to the previous works accumulated in the field of structural RNA biology. Finally, we will also discuss how high-throughput SHAPE (hSHAPE) paved the way for the development of sophisticated RNA structural techniques.},
keywords = {Capillary electrophoresis, chemical probe, enzymatic probe, high-throughput sequencing, MARQUET, mutational profiling, PAILLART, RNA, SHAPE, structure, Unité ARN},
pubstate = {published},
tppubtype = {article}
}
Wilhelm M., Fishman J. A., Pontikis R., Aubertin A. M., Wilhelm F. X.
Susceptibility of recombinant porcine endogenous retrovirus reverse transcriptase to nucleoside and non-nucleoside inhibitors Journal Article
In: Cell Mol Life Sci, vol. 59, no. 12, pp. 2184-90, 2002, (1420-682x Journal Article).
Abstract | BibTeX | Tags: Acid, Amino, Animals, Calf, Chloride/metabolism, Chlorides/metabolism, Cloning, Compounds/metabolism, Data, DNA, DNA-Directed, endogenous, Gov't, H, Human, Inhibitors/*pharmacology, Magnesium, Manganese, Molecular, Non-U.S., Nucleosides/chemistry/*metabolism, P.H.S., Polymerase/chemistry/genetics/*metabolism, Polymerase/metabolism, Proteins/metabolism, Recombinant, Retroviruses/*enzymology, Reverse, Ribonuclease, RNA-Directed, Sequence, Sodium, structure, Support, Swine, Thymus/metabolism, Transcriptase, U.S.
@article{,
title = {Susceptibility of recombinant porcine endogenous retrovirus reverse transcriptase to nucleoside and non-nucleoside inhibitors},
author = { M. Wilhelm and J. A. Fishman and R. Pontikis and A. M. Aubertin and F. X. Wilhelm},
year = {2002},
date = {2002-01-01},
journal = {Cell Mol Life Sci},
volume = {59},
number = {12},
pages = {2184-90},
abstract = {Transplantation of organs, tissues or cells from pigs to humans could be a potential solution to the shortage of human organs for transplantation. Porcine endogenous retroviruses (PERVs) remain a major safety concern for porcine xenotransplantation. Thus, finding drugs that could be used as virological prophylaxis (or therapy) against PERV replication would be desirable. One of the most effective ways to block retroviral multiplication is to inhibit the enzyme reverse transcriptase (RT) which catalyzes the reverse transcription of viral RNA to proviral double-stranded DNA. We report here the cloning and expression of PERV RT and its susceptibility to several inhibitors. Our data demonstrate PERV susceptibility in vitro to the triphosphorylated nucleoside analog of zidovudine (AZT) and to ddGTP and to a lesser extent to ddTTP but almost no susceptibility to the non-nucleoside RT inhibitors tested.},
note = {1420-682x
Journal Article},
keywords = {Acid, Amino, Animals, Calf, Chloride/metabolism, Chlorides/metabolism, Cloning, Compounds/metabolism, Data, DNA, DNA-Directed, endogenous, Gov't, H, Human, Inhibitors/*pharmacology, Magnesium, Manganese, Molecular, Non-U.S., Nucleosides/chemistry/*metabolism, P.H.S., Polymerase/chemistry/genetics/*metabolism, Polymerase/metabolism, Proteins/metabolism, Recombinant, Retroviruses/*enzymology, Reverse, Ribonuclease, RNA-Directed, Sequence, Sodium, structure, Support, Swine, Thymus/metabolism, Transcriptase, U.S.},
pubstate = {published},
tppubtype = {article}
}
Moine H., Mandel J. L.
Biomedicine. Do G quartets orchestrate fragile X pathology? Journal Article
In: Science, vol. 294, no. 5551, pp. 2487-8, 2001, (0036-8075 Journal Article).
BibTeX | Tags: Acid, Analysis, Animals, Array, Binding, Brain/metabolism, Conformation, Crystallography, Expression, Fragile, Gene, Genetic, Human, Messenger/*chemistry/genetics/*metabolism, Mice, Nerve, Nucleic, Oligonucleotide, Protein, Proteins/chemistry/genetics/*metabolism, Regions, Regulation, RNA, Sequence, Sites, structure, Synapses/physiology, Syndrome/genetics/*metabolism, Tertiary, Tissue, Translation, Untranslated, X, X-Ray
@article{,
title = {Biomedicine. Do G quartets orchestrate fragile X pathology?},
author = { H. Moine and J. L. Mandel},
year = {2001},
date = {2001-01-01},
journal = {Science},
volume = {294},
number = {5551},
pages = {2487-8},
note = {0036-8075
Journal Article},
keywords = {Acid, Analysis, Animals, Array, Binding, Brain/metabolism, Conformation, Crystallography, Expression, Fragile, Gene, Genetic, Human, Messenger/*chemistry/genetics/*metabolism, Mice, Nerve, Nucleic, Oligonucleotide, Protein, Proteins/chemistry/genetics/*metabolism, Regions, Regulation, RNA, Sequence, Sites, structure, Synapses/physiology, Syndrome/genetics/*metabolism, Tertiary, Tissue, Translation, Untranslated, X, X-Ray},
pubstate = {published},
tppubtype = {article}
}
Bergdoll M., Eltis L. D., Cameron A. D., Dumas P., Bolin J. T.
All in the family: structural and evolutionary relationships among three modular proteins with diverse functions and variable assembly Journal Article
In: Protein Sci, vol. 7, no. 8, pp. 1661-70, 1998, (0961-8368 Journal Article).
Abstract | BibTeX | Tags: *Acetyltransferases, *Evolution, Acid, Amino, Bacterial, Burkholderia/*chemistry, Crystallography, Data, Genetic, Gov't, Homology, Human, Lactoylglutathione, Lyase/*chemistry, Models, Molecular, Non-U.S., Oxygenases/chemistry, P.H.S., Phylogeny, Protein, Proteins/*chemistry, Secondary, Sequence, structure, Support, U.S., X-Ray
@article{,
title = {All in the family: structural and evolutionary relationships among three modular proteins with diverse functions and variable assembly},
author = { M. Bergdoll and L. D. Eltis and A. D. Cameron and P. Dumas and J. T. Bolin},
year = {1998},
date = {1998-01-01},
journal = {Protein Sci},
volume = {7},
number = {8},
pages = {1661-70},
abstract = {The crystal structures of three proteins of diverse function and low sequence similarity were analyzed to evaluate structural and evolutionary relationships. The proteins include a bacterial bleomycin resistance protein, a bacterial extradiol dioxygenase, and human glyoxalase I. Structural comparisons, as well as phylogenetic analyses, strongly indicate that the modern family of proteins represented by these structures arose through a rich evolutionary history that includes multiple gene duplication and fusion events. These events appear to be historically shared in some cases, but parallel and historically independent in others. A significant early event is proposed to be the establishment of metal-binding in an oligomeric ancestor prior to the first gene fusion. Variations in the spatial arrangements of homologous modules are observed that are consistent with the structural principles of three-dimensional domain swapping, but in the unusual context of the formation of larger monomers from smaller dimers or tetramers. The comparisons support a general mechanism for metalloprotein evolution that exploits the symmetry of a homooligomeric protein to originate a metal binding site and relies upon the relaxation of symmetry, as enabled by gene duplication, to establish and refine specific functions.},
note = {0961-8368
Journal Article},
keywords = {*Acetyltransferases, *Evolution, Acid, Amino, Bacterial, Burkholderia/*chemistry, Crystallography, Data, Genetic, Gov't, Homology, Human, Lactoylglutathione, Lyase/*chemistry, Models, Molecular, Non-U.S., Oxygenases/chemistry, P.H.S., Phylogeny, Protein, Proteins/*chemistry, Secondary, Sequence, structure, Support, U.S., X-Ray},
pubstate = {published},
tppubtype = {article}
}
Friant S., Heyman T., Poch O., Wilhelm M., Wilhelm F. X.
Sequence comparison of the Ty1 and Ty2 elements of the yeast genome supports the structural model of the tRNAiMet-Ty1 RNA reverse transcription initiation complex Journal Article
In: Yeast, vol. 13, no. 7, pp. 639-45, 1997, (0749-503x Journal Article).
Abstract | BibTeX | Tags: *Sequence, Acid, Alignment, Amino, Analysis, Base, Data, DNA, Elements/*genetics, Fungal/genetics, Gov't, Met/*chemistry/*genetics, Molecular, Non-U.S., RNA, Sequence, structure, Support, Transfer, Transposable, Yeasts/*genetics
@article{,
title = {Sequence comparison of the Ty1 and Ty2 elements of the yeast genome supports the structural model of the tRNAiMet-Ty1 RNA reverse transcription initiation complex},
author = { S. Friant and T. Heyman and O. Poch and M. Wilhelm and F. X. Wilhelm},
year = {1997},
date = {1997-01-01},
journal = {Yeast},
volume = {13},
number = {7},
pages = {639-45},
abstract = {In the reverse transcription initiation complex of the yeast Ty1 retrotransposon, interaction between the template RNA and primer tRNAiMet is not limited to base pairing of the primer binding site (PBS) with ten nucleotides at the 3' end of tRNAiMet, but three regions named boxes O, 1 and 2.1 interact with the T and D stems and loops of tRNAiMet. Sequence comparison of 33 Ty1 elements and 13 closely related Ty2 elements found in the yeast genome shows that the nucleotide sequence of all elements is highly conserved in the region spanning the PBS and the three boxes. Since the domain of the template RNA encodes a portion of protein TyA, we have calculated its amino acid profile and its nucleotide profile to evaluate the role played by nucleotide sequence conservation in the selection for TyA function and in the maintenance of base pairing interactions for the priming function of Ty1 RNA. Our results show that the nucleotide sequence conservation of Ty1 RNA is constrained not only by selection for Ty1 function but also by maintenance of a given nucleotide sequence able to base pair with the tRNAiMet in the primer-template initiation complex.},
note = {0749-503x
Journal Article},
keywords = {*Sequence, Acid, Alignment, Amino, Analysis, Base, Data, DNA, Elements/*genetics, Fungal/genetics, Gov't, Met/*chemistry/*genetics, Molecular, Non-U.S., RNA, Sequence, structure, Support, Transfer, Transposable, Yeasts/*genetics},
pubstate = {published},
tppubtype = {article}
}
Friant S., Heyman T., Wilhelm M. L., Wilhelm F. X.
Extended interactions between the primer tRNAi(Met) and genomic RNA of the yeast Ty1 retrotransposon Journal Article
In: Nucleic Acids Res, vol. 24, no. 3, pp. 441-9, 1996, (0305-1048 Journal Article).
Abstract | BibTeX | Tags: Acid, Base, cerevisiae, Conformation, Data, Gov't, Met/genetics/*metabolism, Molecular, Mutation, Non-U.S., Nucleic, Retroelements/*genetics, RNA, RNA/genetics/*metabolism, Saccharomyces, Sequence, structure, Support, Transfer
@article{,
title = {Extended interactions between the primer tRNAi(Met) and genomic RNA of the yeast Ty1 retrotransposon},
author = { S. Friant and T. Heyman and M. L. Wilhelm and F. X. Wilhelm},
year = {1996},
date = {1996-01-01},
journal = {Nucleic Acids Res},
volume = {24},
number = {3},
pages = {441-9},
abstract = {Reverse transcription of the yeast Ty1 retrotransposon is primed by tRNAi(Met) base paired to the primer binding site near the 5'-end of Ty1 genomic RNA. To understand the molecular basis of the tRNAi(Met)-Ty1 RNA interaction the secondary structure of the binary complex was analysed. Enzymatic probes were used to test the conformation of tRNAi(Met) and of Ty1 RNA in the free form and in the complex. A secondary structure model of the tRNAi(Met) Ty1 RNA complex consistent with the probing data was constructed with the help of a computer program. The model shows that besides interactions between the primer binding site and the last 10 nt at the 3'-end of tRNAi(Met), three short regions of Ty1 RNA named boxes 0, 1 and 2.1 interact with the T and D stems and loops of tRNAiMet. Mutations were made in the boxes or in the complementary sequences of tRNAi(Met) to study the contribution of these sequences to formation of the complex. We find that interaction with at least one of the two boxes 0 or 1 is absolutely required for efficient annealing of the two RNAs. Sequence comparison showing that the primary sequence of the boxes is strictly conserved in Ty1 and Ty2 elements and previously published in vivo results underline the functional importance of the primary sequence of the boxes and suggest that extended interactions between genomic Ty1 RNA and the primary tRNAi(Met) play a role in the reverse transcription pathway.},
note = {0305-1048
Journal Article},
keywords = {Acid, Base, cerevisiae, Conformation, Data, Gov't, Met/genetics/*metabolism, Molecular, Mutation, Non-U.S., Nucleic, Retroelements/*genetics, RNA, RNA/genetics/*metabolism, Saccharomyces, Sequence, structure, Support, Transfer},
pubstate = {published},
tppubtype = {article}
}
de Barros J. P. Pais, Keith G., Adlouni C. El, Glasser A. L., Mack G., Dirheimer G., Desgres J.
2'-O-methyl-5-formylcytidine (f5Cm), a new modified nucleotide at the 'wobble' of two cytoplasmic tRNAs Leu (NAA) from bovine liver Journal Article
In: Nucleic Acids Res, vol. 24, no. 8, pp. 1489-96, 1996, (0305-1048 Journal Article).
Abstract | BibTeX | Tags: &, Acid, Acyl/*chemistry/isolation, Amino, Animals, Base, Borohydrides/chemistry, Cattle, Cells, Conformation, Cytidine/*analogs, Cytoplasm, Data, derivatives/chemistry/isolation, Fragmentography, Gov't, Hela, Human, Liver/*chemistry, Mass, Molecular, Non-U.S., Nucleic, purification, RNA, Sequence, structure, Support, Transfer
@article{,
title = {2'-O-methyl-5-formylcytidine (f5Cm), a new modified nucleotide at the 'wobble' of two cytoplasmic tRNAs Leu (NAA) from bovine liver},
author = { J. P. Pais de Barros and G. Keith and C. El Adlouni and A. L. Glasser and G. Mack and G. Dirheimer and J. Desgres},
year = {1996},
date = {1996-01-01},
journal = {Nucleic Acids Res},
volume = {24},
number = {8},
pages = {1489-96},
abstract = {The nucleotide analysis of a cytoplasmic tRNA(Leu) isolated from bovine liver revealed the presence of an unknown modified nucleotide N. The corresponding N nucleoside was isolated by different enzymatic and chromatographic protocols from a partially purified preparation of this tRNA(Leu). Its chemical characterization was determined from its chromatographic properties, UV-absorption spectroscopy and mass spectrometric measurements, as well as from those of the borohydride reduced N nucleoside and its etheno-trimethylsilyl derivative. The structure of N was established as 2'-O-methyl-5-formylcytidine (f5CM), and its reduced derivative as 2'-O-methyl-5-hydroxy-methylcytidine (om5Cm). By sequencing the bovine liver tRNA(Leu), the structure of the anticodon was determined as f5CmAA. In addition, the nucleotide sequence showed two primary structures differing only by the nucleotide 47c which is either uridine or adenosine. The two slightly differing bovine liver tRNAs-Leu(f5CmAA) are the only tRNAs so far sequenced which contain f5Cm. The role of such a modified cytidine at the first position of the anticodon is discussed in terms of decoding properties for the UUG and UUA leucine codons. Recently, precise evidence was obtained for the presence of f5Cm at the same position in tRNAs(Leu)(NAA) isolated from rabbit and lamb liver. Therefore, the 2'-O-methyl-5-formyl modification of cytidine at position 34 could be a general feature of cytoplasmic tRNAs(Leu)(NAA) in mammals.},
note = {0305-1048
Journal Article},
keywords = {&, Acid, Acyl/*chemistry/isolation, Amino, Animals, Base, Borohydrides/chemistry, Cattle, Cells, Conformation, Cytidine/*analogs, Cytoplasm, Data, derivatives/chemistry/isolation, Fragmentography, Gov't, Hela, Human, Liver/*chemistry, Mass, Molecular, Non-U.S., Nucleic, purification, RNA, Sequence, structure, Support, Transfer},
pubstate = {published},
tppubtype = {article}
}
Dumas P., Bergdoll M., Cagnon C., Masson J. M.
Crystal structure and site-directed mutagenesis of a bleomycin resistance protein and their significance for drug sequestering Journal Article
In: EMBO J, vol. 13, no. 11, pp. 2483-92, 1994, (0261-4189 Journal Article).
Abstract | BibTeX | Tags: *Acetyltransferases, &, Acid, Amino, Bacterial, Bacterial/*genetics, Base, Binding, Bleomycin/*metabolism/pharmacology, Conformation, Crystallization, Crystallography, Data, Drug, Fusion, Genes, Gov't, Microbial/genetics, Models, Molecular, Mutagenesis, Non-U.S., Protein, Proteins/*chemistry/genetics/isolation, Proteins/isolation, purification, purification/metabolism, Recombinant, Relationship, Resistance, Secondary, Sequence, Site-Directed, Sites, Structural, structure, Structure-Activity, Support, X-Ray
@article{,
title = {Crystal structure and site-directed mutagenesis of a bleomycin resistance protein and their significance for drug sequestering},
author = { P. Dumas and M. Bergdoll and C. Cagnon and J. M. Masson},
year = {1994},
date = {1994-01-01},
journal = {EMBO J},
volume = {13},
number = {11},
pages = {2483-92},
abstract = {The antibiotic bleomycin, a strong DNA cutting agent, is naturally produced by actinomycetes which have developed a resistance mechanism against such a lethal compound. The crystal structure, at 2.3 A resolution, of a bleomycin resistance protein of 14 kDa reveals a structure in two halves with the same alpha/beta fold despite no sequence similarity. The crystal packing shows compact dimers with a hydrophobic interface and involved in mutual chain exchange. Two independent solution studies (analytical centrifugation and light scattering) showed that this dimeric form is not a packing artefact but is indeed the functional one. Furthermore, light scattering also showed that one dimer binds two antibiotic molecules as expected. A crevice located at the dimer interface, as well as the results of a site-directed mutagenesis study, led to a model wherein two bleomycin molecules are completely sequestered by one dimer. This provides a novel insight into antibiotic resistance due to drug sequestering, and probably also into drug transport and excretion.},
note = {0261-4189
Journal Article},
keywords = {*Acetyltransferases, &, Acid, Amino, Bacterial, Bacterial/*genetics, Base, Binding, Bleomycin/*metabolism/pharmacology, Conformation, Crystallization, Crystallography, Data, Drug, Fusion, Genes, Gov't, Microbial/genetics, Models, Molecular, Mutagenesis, Non-U.S., Protein, Proteins/*chemistry/genetics/isolation, Proteins/isolation, purification, purification/metabolism, Recombinant, Relationship, Resistance, Secondary, Sequence, Site-Directed, Sites, Structural, structure, Structure-Activity, Support, X-Ray},
pubstate = {published},
tppubtype = {article}
}
Glasser A. L., el Adlouni C., Keith G., Sochacka E., Malkiewicz A., Santos M., Tuite M. F., Desgres J.
Presence and coding properties of 2'-O-methyl-5-carbamoylmethyluridine (ncm5Um) in the wobble position of the anticodon of tRNA(Leu) (U*AA) from brewer's yeast Journal Article
In: FEBS Lett, vol. 314, no. 3, pp. 381-5, 1992, (0014-5793 Journal Article).
Abstract | BibTeX | Tags: *Anticodon, &, Analysis, cerevisiae/*genetics, Chromatography, derivatives/analysis/chemistry/genetics, Fungal, Fungal/genetics, Gov't, high, Leu/*genetics, liquid, Mass, Molecular, Non-U.S., Pressure, Proteins/biosynthesis, RNA, Saccharomyces, Spectrophotometry, Spectrum, structure, Support, Transfer, Ultraviolet, Uridine/*analogs
@article{,
title = {Presence and coding properties of 2'-O-methyl-5-carbamoylmethyluridine (ncm5Um) in the wobble position of the anticodon of tRNA(Leu) (U*AA) from brewer's yeast},
author = { A. L. Glasser and C. el Adlouni and G. Keith and E. Sochacka and A. Malkiewicz and M. Santos and M. F. Tuite and J. Desgres},
year = {1992},
date = {1992-01-01},
journal = {FEBS Lett},
volume = {314},
number = {3},
pages = {381-5},
abstract = {The unknown modified nucleoside U* has been isolated by enzymatic and HPLC protocols from tRNA(Leu) (U*AA) recently discovered in brewer's yeast. The pure U* nucleoside has been characterized by electron impact mass spectroscopy, and comparison of its chromatographic and UV-absorption properties with those of appropriate synthetic compounds. The structure of U* was established as 2'-O-methyl-5-carbamoylmethyluridine (ncm5Um). The yeast tRNA(Leu) (U*AA) is the only tRNA so far sequenced which has been shown to contain ncm5Um. The location of such a modified uridine at the first position of the anticodon restricts the decoding property to A of the leucine UUA codon.},
note = {0014-5793
Journal Article},
keywords = {*Anticodon, &, Analysis, cerevisiae/*genetics, Chromatography, derivatives/analysis/chemistry/genetics, Fungal, Fungal/genetics, Gov't, high, Leu/*genetics, liquid, Mass, Molecular, Non-U.S., Pressure, Proteins/biosynthesis, RNA, Saccharomyces, Spectrophotometry, Spectrum, structure, Support, Transfer, Ultraviolet, Uridine/*analogs},
pubstate = {published},
tppubtype = {article}
}