Imaging

@article{,

title = {Yeast serine isoacceptor tRNAs: variations of their content as a function of growth conditions and primary structure of the minor tRNA(Ser)GCU},

author = { T. Heyman and B. Agoutin and C. Fix and G. Dirheimer and G. Keith},

year  = {1994},

date = {1994-01-01},

journal = {FEBS Lett},

volume = {347},

number = {2-3},

pages = {143-6},

abstract = {The primary structure of Saccharomyces cerevisiae tRNA(Ser)GCU is presented (EMBL database accession No. X74268 S. cerevisiae tRNA-Ser). In addition, quantitation of the relative amounts of serine isoaccepting tRNAs in yeast grown on different media showed that the minor tRNA(Ser)GCU decreased while the major tRNA(Ser)AGA increased as the growth rate and the cellular protein content increased. The minor species, tRNA(Ser)CGA and tRNA(Ser)UGA, were not separated by our gel system, however, taken together they appeared to vary in the same way as tRNA(Ser)GCU. These data suggest a growth rate dependence of yeast tRNAs similar to that previously described for E. coli tRNAs.},

note = {0014-5793 

Journal Article},

keywords = {&, Acid, Anticodon, Base, cerevisiae/*genetics/*growth, Conformation, Culture, Data, development, Fungal/*chemistry, Galactose, Hybridization, Media, Molecular, Nucleic, Probes, RNA, Saccharomyces, Sequence, Ser/analysis/*chemistry, Transfer, Transfer/*chemistry},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Yeast Ty1 retrotransposon: the minus-strand primer binding site and a cis-acting domain of the Ty1 RNA are both important for packaging of primer tRNA inside virus-like particles},

author = { M. Wilhelm and F. X. Wilhelm and G. Keith and B. Agoutin and T. Heyman},

year  = {1994},

date = {1994-01-01},

journal = {Nucleic Acids Res},

volume = {22},

number = {22},

pages = {4560-5},

abstract = {Reverse transcription of the yeast retrotransposon Ty1 is primed by the cytoplasmic initiator methionine tRNA (tRNA(iMet)). The primer tRNA(iMet) is packaged inside virus-like particles (VLPs) and binds to a 10 nucleotides minus-strand primer binding site, the (-)PBS, complementary to its 3' acceptor stem. We have found that three short sequences of the Ty1 RNA (box 1, box 2.1 and box 2.2) located 3' to the (-)PBS are complementary to other regions of the primer tRNA(iMet) (T psi C and DHU stems and loops). Reconstitution of reverse transcription in vitro with T7 transcribed Ty1 RNA species and tRNA(iMet) purified from yeast cells shows that the boxes do not affect the efficiency of reverse transcription. Thus the role of the boxes on packaging of the primer tRNA(iMet) into the VLPs was investigated by analysing the level of tRNA(iMet) packaged into mutant VLPs. Specific nucleotide changes in the (-)PBS or in the boxes that do not change the protein coding sequence but disrupt the complementarity with the primer tRNA(iMet) within the VLPs. We propose that base pairing between the primer tRNA(iMet) and the Ty1 RNA is of major importance for tRNA(iMet) packaging into the VLPs. Moreover the intactness of the boxes is essential for retrotransposition as shown by the transposition defect of a Ty1 element harboring an intact (-)PBS and mutated boxes.},

note = {0305-1048 

Journal Article},

keywords = {Acid, Amino, Base, Binding, cerevisiae/*genetics, Cloning, Data, Fungal/*genetics, Genetic, Gov't, Met/*genetics, Molecular, Mutation/physiology, Non-U.S., Retroelements/*genetics/physiology, Retroviridae/genetics, RNA, RNA/*genetics, Saccharomyces, Sequence, Sites, Support, Transcription, Transfer},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Yeast Ty1 retrotransposon: the minus-strand primer binding site and a cis-acting domain of the Ty1 RNA are both important for packaging of primer tRNA inside virus-like particles},

author = {M Wilhelm and F X Wilhelm and G Keith and B Agoutin and T Heyman},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7527135},

isbn = {7527135},

year  = {1994},

date = {1994-01-01},

journal = {Nucleic Acids Res},

volume = {22},

number = {22},

pages = {4560-4565},

abstract = {Reverse transcription of the yeast retrotransposon Ty1 is primed by the cytoplasmic initiator methionine tRNA (tRNA(iMet)). The primer tRNA(iMet) is packaged inside virus-like particles (VLPs) and binds to a 10 nucleotides minus-strand primer binding site, the (-)PBS, complementary to its 3' acceptor stem. We have found that three short sequences of the Ty1 RNA (box 1, box 2.1 and box 2.2) located 3' to the (-)PBS are complementary to other regions of the primer tRNA(iMet) (T psi C and DHU stems and loops). Reconstitution of reverse transcription in vitro with T7 transcribed Ty1 RNA species and tRNA(iMet) purified from yeast cells shows that the boxes do not affect the efficiency of reverse transcription. Thus the role of the boxes on packaging of the primer tRNA(iMet) into the VLPs was investigated by analysing the level of tRNA(iMet) packaged into mutant VLPs. Specific nucleotide changes in the (-)PBS or in the boxes that do not change the protein coding sequence but disrupt the complementarity with the primer tRNA(iMet) within the VLPs. We propose that base pairing between the primer tRNA(iMet) and the Ty1 RNA is of major importance for tRNA(iMet) packaging into the VLPs. Moreover the intactness of the boxes is essential for retrotransposition as shown by the transposition defect of a Ty1 element harboring an intact (-)PBS and mutated boxes.},

note = {0305-1048 

Journal Article},

keywords = {Amino Acid Sequence  Base Sequence  Binding Sites  Cloning, Fungal/*genetics  RNA, Genetic, Met/*genetics  Retroelements/*genetics/physiology  Retroviridae/genetics  Saccharomyces cerevisiae/*genetics  Support, Molecular  Molecular Sequence Data  Mutation/physiology  RNA/*genetics  RNA, Non-U.S. Gov't  Transcription, Transfer, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Intron-dependent formation of pseudouridines in the anticodon of Saccharomyces cerevisiae minor tRNA(Ile)},

author = {Z Szweykowska-Kulinska and B Senger and G Keith and F Fasiolo and H Grosjean},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7925304},

isbn = {7925304},

year  = {1994},

date = {1994-01-01},

journal = {EMBO J},

volume = {13},

number = {19},

pages = {4636-4644},

abstract = {We have isolated and sequenced the minor species of tRNA(Ile) from Saccharomyces cerevisiae. This tRNA contains two unusual pseudouridines (psi s) in the first and third positions of the anticodon. As shown earlier by others, this tRNA derives from two genes having an identical 60 nt intron. We used in vitro procedures to study the structural requirements for the conversion of the anticodon uridines to psi 34 and psi 36. We show here that psi 34/psi 36 modifications require the presence of the pre-tRNA(Ile) intron but are not dependent upon the particular base at any single position of the anticodon. The conversion of U34 to psi 34 occurs independently from psi 36 synthesis and vice versa. However, psi 34 is not formed when the middle and the third anticodon bases of pre-tRNA(Ile) are both substituted to yield ochre anticodon UUA. This ochre pre-tRNA(Ile) mutant has the central anticodon uridine modified to psi 35 as is the case for S.cerevisiae SUP6 tyrosine-inserting ochre suppressor tRNA. In contrast, neither the first nor the third anticodon pseudouridine is formed, when the ochre (UUA) anticodon in the pre-tRNA(Tyr) is substituted with the isoleucine UAU anticodon. A synthetic mini-substrate consisting of the anticodon stem and loop and the wild-type intron of pre-tRNA(Ile) is sufficient to fully modify the anticodon U34 and U36 into psi s. This is the first example of the tRNA intron sequence, rather than the whole tRNA or pre-tRNA domain, being the main determinant of nucleoside modification.},

note = {0261-4189 

Journal Article},

keywords = {Anticodon/*metabolism  Base Sequence  Introns/*physiology  Molecular Sequence Data  Nucleic Acid Conformation  Pseudouridine/*biosynthesis  RNA Processing, Fungal/*metabolism  RNA, Ile/*metabolism  Saccharomyces cerevisiae/*genetics  Support, Non-U.S. Gov't, Post-Transcriptional/physiology  RNA, Transfer, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Base modification pattern at the wobble position of Xenopus selenocysteine tRNA(Sec)},

author = {C Sturchler and A Lescure and G Keith and P Carbon and A Krol},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8031393},

isbn = {8031393},

year  = {1994},

date = {1994-01-01},

journal = {Nucleic Acids Res},

volume = {22},

number = {8},

pages = {1354-1358},

abstract = {We examined the base modification pattern of Xenopus tRNA(Sec) using microinjection into Xenopus oocytes, with particular focus on the wobble base U34 at the first position of the anticodon. We found that U34 becomes modified to mcm5U34 (5-methylcarboxymethyluridine) in the oocyte cytoplasm in a rather complex manner. When the tRNA(Sec) gene is injected into Xenopus oocyte nuclei, psi 55 and m1A58 are readily obtained, but not mcm5U34. This will appear only upon cytoplasmic injection of the gene product arising from the first nuclear injection. In contrast, tRNA(Sec) produced by in vitro transcription with T7 RNA polymerase readily acquires i6A37, psi 55, m1A58, and mcm5U34. The latter is obtained after direct nuclear or cytoplasmic injections. It has been reported by others that mcm5Um, a 2'-O-methylated derivative of mcm5U34, also exists in rat and bovine tRNA(Sec). With both the gene product and the in vitro transcript, and using the sensitive RNase T2 assay, we were unable to detect under our conditions the presence of a dinucleotide carrying mcm5Um and that would be therefore refractory to hydrolysis. We showed that the unusual mcm5U acquisition pathway does not result from impairment of nucleocytoplasmic transport. Rather, these data can be interpreted to mean that the modification is performed by a tRNA(Sec) specific enzyme, limiting in the oocyte cytoplasm.},

note = {0305-1048 

Journal Article},

keywords = {Amino Acid-Specific/chemistry/*genetics/metabolism  Selenocysteine/*metabolism  Support, Animals  *Anticodon  Base Composition  Base Sequence  Microinjections  Molecular Sequence Data  Mutagenesis  Nucleic Acid Conformation  RNA, LESCURE, Non-U.S. Gov't  Uridine  Xenopus laevis, Transfer, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Histidylation by yeast HisRS of tRNA or tRNA-like structure relies on residues -1 and 73 but is dependent on the RNA context},

author = {J Rudinger and C Florentz and R Giege},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7800496},

isbn = {7800496},

year  = {1994},

date = {1994-01-01},

journal = {Nucleic Acids Res},

volume = {22},

number = {23},

pages = {5031-5037},

abstract = {Residue G-1 and discriminator base C73 are the major histidine identity elements in prokaryotes. Here we evaluate the importance of these two nucleotides in yeast histidine aminoacylation identity. Deletion of G-1 in yeast tRNA(His) transcript leads to a drastic loss of histidylation specificity (about 500-fold). Mutation of discriminator base A73, common to all yeast tRNA(His) species, into G73 has a more moderate but still significant effect with a 22-fold decrease in histidylation specificity. Changes at position 36 in the anticodon loop has negligible effect on histidylation. The role of residues -1 and 73 for specific aminoacylation by yeast HisRS was further investigated by studying the histidylation capacities of seven minihelices derived from the Turnip Yellow Mosaic Virus tRNA-like structure. Changes in the nature of nucleotides -1 and 73 modulate this activity but do not suppress it. The optimal mini-substrate for HisRS presents a G.A mismatch at the position equivalent to residues G-1.A73 in yeast tRNA(His), confirms the importance of this structural feature in yeast histidine identity. The fact that the minisubstrates contain a pseudoknot in which position -1 is mimicked by an internal nucleotide from the pseudoknot highlights further the necessity of a stacking interaction of this position over the amino acid accepting branch of the tRNA during the aminoacylation process. Individual transplantation of G-1 or A73 into yeast tRNA(Asp) transcript improves the histidylation efficiency of the engineered tRNA(Asp). However, a tRNA(Asp) transcript presenting simultaneously both residues G-1 and A73 becomes a less good substrate for HisRS, suggesting the importance of the structural context and/or the presence of antideterminants for an optimal expression of these two identity elements.},

note = {0305-1048 

Journal Article},

keywords = {Anticodon/genetics  Base Sequence  Genes, Asp/genetics  RNA, FLORENTZ, His/*chemistry/*genetics  RNA, Non-U.S. Gov't  Tymovirus/genetics  Yeasts/enzymology, Synthetic/genetics  Histidine-tRNA Ligase/*metabolism  Kinetics  Molecular Sequence Data  *Nucleic Acid Conformation  Point Mutation/physiology  RNA, Transfer, Unité ARN, Viral/metabolism  Support},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {A single methyl group prevents the mischarging of a tRNA},

author = {J Putz and C Florentz and F Benseler and R Giege},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=7634096},

isbn = {7634096},

year  = {1994},

date = {1994-01-01},

journal = {Nat Struct Biol},

volume = {1},

number = {9},

pages = {580-582},

note = {1072-8368 

Letter},

keywords = {Arginine/*genetics  Arginine-tRNA Ligase/metabolism  Base Sequence  Methylation  Molecular Sequence Data  Mutation  Nucleic Acid Conformation  RNA, Asp/chemistry/*genetics/metabolism, FLORENTZ, Transfer, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Molecular recognition of the identity-determinant set of isoleucine transfer RNA from Escherichia coli},

author = {O Nureki and T Niimi and T Muramatsu and H Kanno and T Kohno and C Florentz and R Giege and S Yokoyama},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8114089},

isbn = {8114089},

year  = {1994},

date = {1994-01-01},

journal = {J Mol Biol},

volume = {236},

number = {3},

pages = {710-724},

abstract = {Molecular recognition of Escherichia coli tRNA(Ile) by the cognate isoleucyl-tRNA synthetase (IleRS) was studied by analyses of chemical footprinting with N-nitroso-N-ethylurea and aminoacylation kinetics of variant tRNA(Ile) transcripts prepared with bacteriophage T7 RNA polymerase. IleRS binds to the acceptor, dihydrouridine (D), and anticodon stems as well as to the anticodon loop. The "complete set" of determinants for the tRNA(Ile) identity consists of most of the nucleotides in the anticodon loop (G34, A35, U36, t6A37 and A38), the discriminator nucleotide (A73), and the base-pairs in the middle of the anticodon, D and acceptor stems (C29.G41, U12.A23 and C4.G69, respectively). As for the tertiary base-pairs, two are indispensable for the isoleucylation activity, whereas the others are dispensable. Correspondingly, some of the phosphate groups of these dispensable tertiary base-pair residues were shown to be exposed to N-nitroso-N-ethylurea when tRNA(Ile) was bound with IleRS. Furthermore, deletion of the T psi C-arm only slightly impaired the tRNA(Ile) activity. Thus, it is proposed that the recognition by IleRS of all the widely distributed identity determinants is coupled with a global conformational change that involves the loosening of a particular set of tertiary base-pairs of tRNA(Ile).},

note = {0022-2836 

Journal Article},

keywords = {Anticodon/chemistry  Base Composition  Base Sequence  Binding Sites  Computer Graphics  Escherichia coli/genetics/*metabolism  Genes, Bacterial  Genes, FLORENTZ, Ile/*chemistry/metabolism  Support, Molecular  Molecular Sequence Data  *Nucleic Acid Conformation  Nucleic Acid Denaturation  RNA, Non-U.S. Gov't, Structural, Synthetic  Isoleucine-tRNA Ligase/*metabolism  Models, Transfer, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Transcription factors required for the expression of Xenopus laevis selenocysteine tRNA in vitro},

author = {W Meissner and I Wanandi and P Carbon and A Krol and K H Seifart},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8127703},

isbn = {8127703},

year  = {1994},

date = {1994-01-01},

journal = {Nucleic Acids Res},

volume = {22},

number = {4},

pages = {553-559},

abstract = {It has previously been reported that transcription in vivo of the tRNA(Sec) gene requires three promoter elements, a PSE and a TATA-box upstream of the coding region which are functionally interchangeable with the U6 snRNA gene counterparts and an internal B-block, resembling that of classical tRNA genes (1). We have established an in vitro transcription system from HeLa cells in which three factors, which are either essential for or stimulate transcription were identified. Apart from the TATA-binding protein TBP, the PSE-binding protein PBP was found to be essentially required for expression of the gene. Depletion of PBP from cell extracts by PSE-oligonucleotides abolished tRNA(Sec) transcription, which could be reconstituted by readdition of partially purified PBP. Addition of increasing amounts of recombinant human TBP to an S100 extract stimulated transcription of the tRNA(Sec), the mouse U6 snRNA and the human Y3 genes, an effect which was not observed in the case of a TATA-less tRNA gene. Purified human TFIIA strongly stimulated tRNA(Sec) transcription in a fashion depending on the concentration of TBP. Surprisingly, partially purified TFIIIC was shown to be dispensable for transcription in vitro and unable to bind the B-block of this gene in vitro, although its sequence matches the consensus for this element. Collectively, these data suggest that the mechanism by which transcription complexes are formed on the tRNA(Sec) gene is dramatically different from that observed for classical tRNA genes and much more resembles that observed for externally controlled pol III genes.},

note = {0305-1048 

Journal Article},

keywords = {Amino Acid-Specific/*genetics  Support, Animals  Base Sequence  DNA-Binding Proteins/*physiology  Human  Molecular Sequence Data  Oligonucleotide Probes  RNA, Genetic  Xenopus laevis, Non-U.S. Gov't  TATA Box  Transcription Factors/*genetics  Transcription, Transfer, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Yeast serine isoacceptor tRNAs: variations of their content as a function of growth conditions and primary structure of the minor tRNA(Ser)GCU},

author = {T Heyman and B Agoutin and C Fix and G Dirheimer and G Keith},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8033992},

isbn = {8033992},

year  = {1994},

date = {1994-01-01},

journal = {FEBS Lett},

volume = {347},

number = {2-3},

pages = {143-146},

abstract = {The primary structure of Saccharomyces cerevisiae tRNA(Ser)GCU is presented (EMBL database accession No. X74268 S. cerevisiae tRNA-Ser). In addition, quantitation of the relative amounts of serine isoaccepting tRNAs in yeast grown on different media showed that the minor tRNA(Ser)GCU decreased while the major tRNA(Ser)AGA increased as the growth rate and the cellular protein content increased. The minor species, tRNA(Ser)CGA and tRNA(Ser)UGA, were not separated by our gel system, however, taken together they appeared to vary in the same way as tRNA(Ser)GCU. These data suggest a growth rate dependence of yeast tRNAs similar to that previously described for E. coli tRNAs.},

note = {0014-5793 

Journal Article},

keywords = {Anticodon  Base Sequence  Culture Media  Galactose  Molecular Sequence Data  Nucleic Acid Conformation  Nucleic Acid Hybridization  RNA Probes  RNA, Fungal/*chemistry  RNA, Ser/analysis/*chemistry  Saccharomyces cerevisiae/*genetics/*growth & development, Transfer, Transfer/*chemistry  RNA, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Identity switches between tRNAs aminoacylated by class I glutaminyl- and class II aspartyl-tRNA synthetases},

author = {M Frugier and D Soll and R Giege and C Florentz},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8060999},

isbn = {8060999},

year  = {1994},

date = {1994-01-01},

journal = {Biochemistry},

volume = {33},

number = {33},

pages = {9912-9921},

abstract = {High-resolution X-ray structures for the tRNA/aminoacyl-tRNA synthetase complexes between Escherichia coli tRNAGln/GlnRS and yeast tRNAAsp/AspRS have been determined. Positive identity nucleotides that direct aminoacylation specificity have been defined in both cases; E. coli tRNAGln identity is governed by 10 elements scattered in the tRNA structure, while specific aminoacylation of yeast tRNAAsp is dependent on 5 positions. Both identity sets are partially overlapping and share 3 nucleotides. Interestingly, the two enzymes belong to two different classes described for aminoacyl-tRNA synthetases. The class I glutaminyl-tRNA synthetase and the class II aspartyl-tRNA synthetase recognize their cognate tRNA from opposite sides. Mutants derived from glutamine and aspartate tRNAs have been created by progressively introducing identity elements from one tRNA into the other one. Glutaminylation and aspartylation assays of the transplanted tRNAs show that identity nucleotides from a tRNA originally aminoacylated by a synthetase from one class are still recognized if they are presented to the enzyme in a structural framework corresponding to a tRNA aminoacylated by a synthetase belonging to the other class. The simple transplantation of the glutamine identity set into tRNAAsp is sufficient to obtain glutaminylatable tRNA, but additional subtle features seem to be important for the complete conversion of tRNAGln in an aspartylatable substrate. This study defines C38 in yeast tRNAAsp as a new identity nucleotide for aspartylation. We show also in this paper that, during the complex formation, aminoacyl-tRNA synthetases are at least partially responsible for conformational changes which involve structural constraints in tRNA molecules.},

note = {0006-2960 

Journal Article},

keywords = {Acylation  Aspartate-tRNA Ligase/chemistry/*metabolism  Base Sequence  Crystallization  Escherichia coli/*enzymology/genetics  Glutamate-tRNA Ligase/chemistry/*metabolism  Kinetics  Molecular Sequence Data  Molecular Structure  Mutation  Nucleic Acid Conformation  RNA, Asp/chemistry/*metabolism  RNA, ERIANI, FLORENTZ, FRUGIER, Gln/chemistry/*metabolism  Saccharomyces cerevisiae/*enzymology/genetics  Support, Non-U.S. Gov't  Support, P.H.S., Transfer, U.S. Gov't, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Synthetic polyamines stimulate in vitro transcription by T7 RNA polymerase},

author = {M Frugier and C Florentz and M W Hosseini and J M Lehn and R Giege},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8052534},

isbn = {8052534},

year  = {1994},

date = {1994-01-01},

journal = {Nucleic Acids Res},

volume = {22},

number = {14},

pages = {2784-2790},

abstract = {The influence of nine synthetic polyamines on in vitro transcription with T7 RNA polymerase has been studied. The compounds used were linear or macrocyclic tetra- and hexaamine, varying in their size, shape and number of protonated groups. Their effect was tested on different types of templates, all presenting the T7 RNA promoter in a double-stranded form followed by sequences encoding short transcripts (25 to 35-mers) either on single- or double-stranded synthetic oligodeoxyribonucleotides. All polyamines used stimulate transcription of both types of templates at levels dependent on their size, shape, protonation degree, and concentration. For each compound, an optimal concentration could be defined; above this concentration, transcription inhibition occurred. Highest stimulation (up to 12-fold) was obtained by the largest cyclic compound called [38]N6C10.},

note = {0305-1048 

Journal Article},

keywords = {Bacteriophage T7/enzymology  Base Sequence  Comparative Study  DNA-Directed RNA Polymerases/drug effects/*metabolism  Kinetics  Molecular Sequence Data  Molecular Structure  Nucleic Acid Conformation  Oligodeoxyribonucleotides  Polyamines/chemistry/*pharmacology  Promoter Regions (Genetics)  RNA, ERIANI, FLORENTZ, FRUGIER, Genetic  Transcription, Genetic/*drug effects, Non-U.S. Gov't  Templates, Transfer, Unité ARN, Val/*biosynthesis/chemistry  Structure-Activity Relationship  Support},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {A histidine accepting tRNA-like fold at the 3'-end of satellite tobacco mosaic virus RNA},

author = {B Felden and C Florentz and A McPherson and R Giege},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8065897},

isbn = {8065897},

year  = {1994},

date = {1994-01-01},

journal = {Nucleic Acids Res},

volume = {22},

number = {15},

pages = {2882-2886},

abstract = {A model of secondary structure is proposed for the 3'-terminal sequence of the satellite tobacco mosaic virus (STMV) RNA on the basis of phylogenetic comparisons with tobacco mosaic virus (TMV) genomic RNA. Sequence homologies and compensatory base changes found between the two related viral RNAs imply that the 3'-end of STMV RNA folds into a tRNA-like domain similar to that found in the TMV RNA. Accordingly, functional assays showed that STMV RNA can be aminoacylated in vitro with histidine by yeast histidyl-tRNA synthetase to plateaus reaching 30%. Histidylation properties of STMV RNA were compared to those of TMV RNA and of a canonical yeast tRNA(His) transcript which both are chargeable to nearly 100% plateau levels. Kinetic data indicate an excellent catalytic efficiency of STMV RNA charging expressed as Vmax/Km ratio, quasi-equivalent to that of TMV RNA, and only 17-fold reduced as compared to that of the yeast tRNAHis transcript. Biological implications of the structural mimicry between the tRNA-like regions of TMV and STMV RNAs are discussed in the light of the relationships of a satellite virus with its helper virus. This is the first report on a chargeable tRNA-like structure at the 3'-end of a satellite virus RNA.},

note = {0305-1048 

Journal Article},

keywords = {Acylation  Base Sequence  Comparative Study  Histidine/*metabolism  Histidine-tRNA Ligase/metabolism  Kinetics  Molecular Sequence Data  *Nucleic Acid Conformation  Phylogeny  RNA, FLORENTZ, His/metabolism  RNA, Non-U.S. Gov't  Tobacco Mosaic Virus/*genetics, Transfer, Transfer/*chemistry  RNA, Unité ARN, Viral/*chemistry  Saccharomyces cerevisiae/enzymology  Sequence Homology  Support},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Solution structure of the 3'-end of brome mosaic virus genomic RNAs. Conformational mimicry with canonical tRNAs},

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=8289279},

isbn = {8289279},

year  = {1994},

date = {1994-01-01},

journal = {J Mol Biol},

volume = {235},

number = {2},

pages = {508-531},

abstract = {The conformation of the last 201 nucleotides located at the 3'-end of brome mosaic virus (BMV) RNAs was investigated in solution using different chemical and enzymatic probes. Bases were probed with dimethylsulfate (which methylates N-1 positions of A, N-3 positions of C and N-7 positions of G), a carbodiimide (which modifies N-1 positions of G and N-3 positions of U) and diethylpyrocarbonate (which modifies N-7 positions of A). Ribonucleases T1, U2 and S1 were used to map unpaired nucleotides and ribonuclease V1 to monitor paired bases or stacked nucleotides. Cleavage or modification sites were detected by gel electrophoresis either indirectly by analyzing DNA sequence patterns generated by primer extension with reverse transcriptase of the modified RNAs or by direct identification within the statistical cleavage patterns of the RNA. On the basis of these biochemical results, an atomic model was built by computer modeling and its stereochemistry refined. The deduced secondary structure of the RNA confirms data previously proposed by others but contains additional base-pairs (A27-U32, A28-G31, G41-A134, G64-C68, U80-A99, G81-A98, G88-U91, G100-U126, U104-U125, G162-G166 and A172-A191), one new tertiary long-range interaction (U103-U164) and a small triple helical conformation with (G41-A134)-A18 and (C42-G133)-A17 interactions. The new secondary structure also indicates the existence of a second pseudoknot involving pairing between residues A181 to A184 and residues U197 to U194, outside the domain conferring tyrosylation ability to BMV RNA. The main outcome from the model stems from its intricate folding, which allows a new assignment for the domains mimicking the anticodon- and D-loop regions of tRNA. Interestingly, the stem and loop region found structurally to be analogous to the anticodon arm of tRNA(Tyr) does not contain the tyrosine anticodon involved in the aminoacylation process. The structural analogies with canonical tRNA(Tyr) illustrate the functional mimicry existing between the BMV RNA structure and canonical tRNA(Tyr) that allows for their efficient aminoacylation by tyrosyl-tRNA synthetase. This structural model rationalizes mutagenic and footprinting data that have established the importance of specific regions of the viral RNA for recognition by its replicase, (ATP,CTP):tRNA nucleotidyl-transferase and yeast tyrosyl-tRNA synthetase. The new fold has biological implications that can be used as a predictive tool for elaborating new experiments.},

note = {0022-2836 

Journal Article},

keywords = {Base Sequence  Bromovirus/*genetics  Computer Simulation  Models, FLORENTZ, Genetic  Models, Molecular  Molecular Sequence Data  Nucleic Acid Conformation  RNA, Non-U.S. Gov't, Transfer, Tyr/*chemistry  RNA, Unité ARN, Viral/*chemistry  Solutions  Support},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Modulation of the suppression efficiency and amino acid identity of an artificial yeast amber isoleucine transfer RNA in Escherichia coli by a G-U pair in the anticodon stem},

author = {V Buttcher and B Senger and S Schumacher and J Reinbolt and F Fasiolo},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8166708},

isbn = {8166708},

year  = {1994},

date = {1994-01-01},

journal = {Biochem Biophys Res Commun},

volume = {200},

number = {1},

pages = {370-377},

abstract = {The artificial amber suppressor corresponding to the major isoleucine tRNA from yeast (pVBt5), when expressed in E. coli, is a poor suppressor of the amber mutation lacIam181-Z. By analysing mutant forms, we could show that this was due to the presence of a U30-G40 wobble pair in the anticodon stem of the yeast tRNA and not to the level of the heterologously expressed tRNA. Efficient suppressors were obtained by restoring a normal U30-A40 or G30-C40 Watson-Crick pair. In vivo the mutant forms are exclusively charged by the bacterial lysyl-tRNA synthetase (LysRS), whereas the original yeast amber tRNA is charged at a low level by E. coli glutaminyl-tRNA synthetase (GlnRS) and LysRS. The inversion of the U30-G40 pair also induces a loss of the Gln identity. We conclude from these experiments that the U30-G40 base pair constitutes a negative determinant for LysRS interaction which operates either at the level of complex formation or at the catalytic step. As no direct contacts are seen between GlnRS and positions 30-40 of the complexed homologous tRNA, the U30-G40 pair of pVBt5 is believed to influence aminoacylation by GlnRS indirectly, probably at the level of the anticodon loop conformation by favouring an optimal apposition of the anticodon nucleotides with the protein.},

note = {0006-291x 

Journal Article},

keywords = {Amino Acyl-tRNA Ligases/metabolism  Anticodon/*genetics  Base Composition  Base Sequence  Chromosomes, Artificial, Bacterial  Guanine  Inversion (Genetics)  Lysine-tRNA Ligase/metabolism  Molecular Sequence Data  Mutagenesis  Nucleic Acid Conformation  Plasmids  RNA, Genetic  Tetrahydrofolate Dehydrogenase/biosynthesis/genetics/isolation &  purification  Uracil, Gln/chemistry/genetics  RNA, Ile/chemistry/*genetics  RNA, Lys/chemistry/*genetics  Saccharomyces cerevisiae/*genetics  *Suppression, Structural, Transfer, Unité ARN, Yeast  Escherichia coli/*genetics  Genes},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Eukaryotic selenocysteine inserting tRNA species support selenoprotein synthesis in Escherichia coli},

author = {C Baron and C Sturchler and X Q Wu and H J Gross and A Krol and A Bock},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8036149},

isbn = {8036149},

year  = {1994},

date = {1994-01-01},

journal = {Nucleic Acids Res},

volume = {22},

number = {12},

pages = {2228-2233},

abstract = {Although the tRNA species directing selenocysteine insertion in prokaryotes differ greatly in their primary structure from that of their eukaryotic homologues they share very similar three-dimensional structures. To analyse whether this conservation of the overall shape of the molecules reflects a conservation of their functional interactions it was tested whether the selenocysteine inserting tRNA species from Homo sapiens supports selenoprotein synthesis in E. coli. It was found that the expression of the human tRNA(Sec) gene in E.coli can complement a lesion in the tRNA(Sec) gene of this organism. Transcripts of the Homo sapiens and Xenopus laevis tRNA(Sec) genes synthesised in vitro were amino-acylated by the E.coli seryl-tRNA ligase although at a very low rate and the resulting seryl-tRNA(Sec) was bound to and converted into selenocysteyl-tRNA(Sec) by the selenocysteine synthase of this organism. Selenocysteyl-tRNA(Sec) from both eukaryotes was able to form a complex with translation factor SELB from E.coli. Although the mechanism of selenocysteine incorporation into seleno-proteins appears to be rather different in E.coli and in vertebrates, we observe here a surprising conservation of functions over an enormous evolutionary distance.},

note = {0305-1048 

Journal Article},

keywords = {Amino Acid-Specific/chemistry/*genetics  Selenocysteine/chemistry  Serine-tRNA Ligase/metabolism  Support, Animals  Bacterial Proteins/metabolism  Base Sequence  Cloning, Molecular  Escherichia coli/*genetics  Genetic Complementation Test  Human  Nucleic Acid Conformation  Peptide Elongation Factors/metabolism  Proteins/*biosynthesis/genetics  RNA, Non-U.S. Gov't  Xenopus laevis, Transfer, Unité ARN},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Rye nuclease I as a tool for structural studies of tRNAs with large variable arms},

author = { C. el Adlouni and G. Keith and G. Dirheimer and J. W. Szarkowski and A. Przykorska},

year  = {1993},

date = {1993-01-01},

journal = {Nucleic Acids Res},

volume = {21},

number = {4},

pages = {941-7},

abstract = {A single-strand-specific nuclease from rye germ (Rn nuclease I) was used for secondary and tertiary structure investigations of tRNAs with large variable arms (class II tRNAs). We have studied the structure in solution of two recently sequenced tRNA(Leu): yeast tRNA(Leu)(ncm5UmAA) and bovine tRNA(Leu)(XmAA) as well as yeast tRNA(Leu)(UAG), tRNA(Leu)(m5CAA) and tRNA(Ser)(IGA). The latter is the only tRNA with a long variable arm for which the secondary and tertiary structure has already been studied by use of chemical probes and computer modelling. The data obtained in this work showed that the general model of class II tRNAs proposed by others for tRNA(Ser) can be extended to tRNAs(Leu) as well. However interesting differences in the structure of tRNAs(Leu) versus tRNA(Ser)(IGA) were also noticed. The main difference was observed in the accessibility of the variable loops to nucleolytic attack of Rn nuclease I: variable loops of all studied tRNA(Leu) species were cut by Rn nuclease I, while that of yeast tRNA(Ser)(IGA) was not. This could be due to differences in stability of the variable arms and the lengths of their loops which are 3 and 4 nucleotides in tRNA(Ser)(IGA) and tRNAs(Leu) respectively.},

note = {0305-1048 

Journal Article},

keywords = {*Nucleotidases, Acid, Animals, Anticodon, Base, Cattle, cereale/*enzymology, cerevisiae, Conformation, Data, Gov't, Leu/chemistry, Molecular, Non-U.S., Nucleic, RNA, Saccharomyces, Secale, Sequence, Ser/chemistry, Support, Transfer, Transfer/*chemistry},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {The primary structure of cytoplasmic initiator tRNA(Met) from Schizosaccharomyces pombe},

author = { G. Keith and J. Heitzler and C. el Adlouni and A. L. Glasser and C. Fix and J. Desgres and G. Dirheimer},

year  = {1993},

date = {1993-01-01},

journal = {Nucleic Acids Res},

volume = {21},

number = {12},

pages = {2949},

note = {0305-1048 

Journal Article},

keywords = {Base, Data, Fungal/*chemistry, Met/*chemistry, Molecular, RNA, Schizosaccharomyces/*genetics, Sequence, Transfer},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {A very poorly expressed tRNA(Ser) is highly concentrated together with replication primer initiator tRNA(Met) in the yeast Ty1 virus-like particles},

author = { P. Pochart and B. Agoutin and C. Fix and G. Keith and T. Heyman},

year  = {1993},

date = {1993-01-01},

journal = {Nucleic Acids Res},

volume = {21},

number = {7},

pages = {1517-21},

abstract = {The analysis of the tRNAs associated to the virus-like particles produced by the Ty1 element revealed the specific packaging of three major tRNA species, in about equal amounts: the replication primer initiator tRNA(Met), the tRNA(Ser)AGA and a tRNA undetected until now as an expressed species in yeast. The latter tRNA is coded by the already described tDNA(Ser)GCT. This tRNA is enriched more than 150 fold in the particles as compared to its content in total cellular tRNA where it represents less than 0.1% (initiator tRNA(Met) and tRNA(Ser)AGA being 11 and 4 fold enriched respectively). This tRNA is the only species coded by the tDNA(Ser)GCT gene which is found in three copies per genome since no other corresponding expressed tRNA could be detected. This gene is thus very poorly expressed. The high concentration of tRNA(Ser)GCU in the particles compared to its very low cellular content led us to consider its possible implication in Ty specific processes.},

note = {0305-1048 

Journal Article},

keywords = {&, Acid, Base, cerevisiae/metabolism, Conformation, Data, development, DNA, Electrophoresis, Elements/*physiology, Gel, Met/metabolism, Molecular, Nucleic, Retroviridae/*growth, RNA, Saccharomyces, Sequence, Ser/*metabolism, Transfer, Transposable, Two-Dimensional, Viral/*metabolism},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Non-standard translational events in Candida albicans mediated by an unusual seryl-tRNA with a 5'-CAG-3' (leucine) anticodon},

author = { M. A. Santos and G. Keith and M. F. Tuite},

year  = {1993},

date = {1993-01-01},

journal = {EMBO J},

volume = {12},

number = {2},

pages = {607-16},

abstract = {From in vitro translation studies we have previously demonstrated the existence of an apparent efficient UAG (amber) suppressor tRNA in the dimorphic fungus Candida albicans (Santos et al., 1990). Using an in vitro assay for termination codon readthrough the tRNA responsible was purified to homogeneity from C.albicans cells. The determined sequence of the purified tRNA predicts a 5'-CAG-3' anticodon that should decode the leucine codon CUG and not the UAG termination codon as originally hypothesized. However, the tRNA(CAG) sequence shows greater nucleotide homology with seryl-tRNAs from the closely related yeast Saccharomyces cerevisiae than with leucyl-tRNAs from the same species. In vitro tRNA-charging studies demonstrated that the purified tRNA(CAG) is charged with Ser. The gene encoding the tRNA was cloned from C.albicans by a PCR-based strategy and DNA sequence analysis confirmed both the structure of the tRNA(CAG) and the absence of any introns in the tRNA gene. The copy number of the tRNA(CAG) gene (1-2 genes per haploid genome) is in agreement with the relatively low abundance (< 0.5% total tRNA) of this tRNA. In vitro translation studies revealed that the purified tRNA(CAG) could induce apparent translational bypass of all three termination codons. However, peptide mapping of in vitro translation products demonstrated that the tRNA(CAG) induces translational misreading in the amino-terminal region of two RNA templates employed, namely the rabbit alpha- and beta-globin mRNAs. These results suggest that the C.albicans tRNA(CAG) is not an 'omnipotent' suppressor tRNA but rather may mediate a novel non-standard translational event in vitro during the translation of the CUG codon. The possible nature of this non-standard translation event is discussed in the context of both the unusual structural features of the tRNA(CAG) and its in vitro behaviour.},

note = {0261-4189 

Journal Article},

keywords = {*Anticodon, *Translation, &, Acid, albicans/*genetics, Base, Candida, Cloning, Conformation, Data, DNA, Fungal, Fungal/chemistry/genetics/isolation, Genes, Genetic, Gov't, Leucine/*genetics, Molecular, Non-U.S., Nucleic, purification, RNA, Sequence, Ser/chemistry/*genetics/isolation, Support, Transfer},

pubstate = {published},

tppubtype = {article}

}

@article{,

title = {Identity elements of tRNA(Trp). Identification and evolutionary conservation},

author = {H Xue and W Shen and R Giege and J T Wong},

url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=8486627},

isbn = {8486627},

year  = {1993},

date = {1993-01-01},

journal = {J Biol Chem},

volume = {268},

number = {13},

pages = {9316-9322},

abstract = {In this study, the varying reactivities of Bacillus subtilis tryptophanyl-tRNA synthetase toward prokaryotic, eukaryotic, and halophile tRNAs were employed to define the potential identity elements on tRNA(Trp). On this basis mutagenesis was performed to obtain, through in vivo heterologous expression in Escherichia coli and in vitro transcription with T7 RNA polymerase, mutant B. subtilis tRNA(Trp) for comparison with the wild-type. These comparisons served to establish G73 and the anticodon as major identity elements, and A1-U72, G5-C68, and A9 as minor identity elements. While the tryptophanyl-tRNA synthetase from B. subtilis and E. coli require G73 to function, replacement of G73 by A73 favors the enzyme from yeast. This change points to the variation of the identity elements for the same amino acid among different organisms. The similarity in these elements between B. subtilis and E. coli tryptophanyl-tRNA synthetase, however, suggests that identity elements on tRNA, like the active centers on enzymes, undergo evolutionary change at slower rates than less essential portions of the macromolecule.},

note = {0021-9258 

Journal Article},

keywords = {Animals  Bacillus subtilis/*genetics  Base Sequence  Cattle  Cloning, Bacterial  Halobacterium/genetics  Kinetics  Liver/physiology  Molecular Sequence Data  Nucleic Acid Conformation  Nucleic Acid Denaturation  RNA, Molecular  Comparative Study  Escherichia coli/*genetics  *Evolution  Genes, Non-U.S. Gov't  Triticum/genetics  Tryptophan-tRNA Ligase/metabolism, Nucleic Acid  Support, Structural, Transfer, Trp/chemistry/*genetics/metabolism  Saccharomyces cerevisiae/genetics  Sequence Homology, Unité ARN},

pubstate = {published},

tppubtype = {article}

}