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2020 |
Théobald-Dietrich, A; de Wijn, R; Rollet, K; Bluhm, A; Rudinger-Thirion, J; Paulus, C; Lorber, B; Thureau, A; Frugier, M; Sauter, C Structural Analysis of RNA by Small-Angle X-ray Scattering Book Chapter Arluison, V; Wien, F (Ed.): RNA Spectroscopy: Methods and Protocols, 2113 , p. 189-215, Springer Protocols, Humana Press, New York, NY, 2020, ISBN: 32006316. Résumé | Liens | BibTeX | Étiquettes: ERIANI, FRUGIER, FRUGIER IRES Integrative structural biology RNA SEC-SAXS Structure tRNA, Unité ARN @inbook{, title = {Structural Analysis of RNA by Small-Angle X-ray Scattering}, author = {A Théobald-Dietrich and R de Wijn and K Rollet and A Bluhm and J Rudinger-Thirion and C Paulus and B Lorber and A Thureau and M Frugier and C Sauter}, editor = {V Arluison and F Wien}, url = {https://pubmed.ncbi.nlm.nih.gov/32006316}, doi = {10.1007/978-1-0716-0278-2_14}, isbn = {32006316}, year = {2020}, date = {2020-01-01}, booktitle = {RNA Spectroscopy: Methods and Protocols}, volume = {2113}, pages = {189-215}, publisher = {Springer Protocols, Humana Press}, address = {New York, NY}, series = {Methods in Molecular Biology}, abstract = {Over the past two decades small-angle X-ray scattering (SAXS) has become a popular method to characterize solutions of biomolecules including ribonucleic acid (RNA). In an integrative structural approach, SAXS is complementary to crystallography, NMR, and electron microscopy and provides information about RNA architecture and dynamics. This chapter highlights the practical advantages of combining size-exclusion chromatography and SAXS at synchrotron facilities. It is illustrated by practical case studies of samples ranging from single hairpins and tRNA to a large IRES. The emphasis is also put on sample preparation which is a critical step of SAXS analysis and on optimized protocols for in vitro RNA synthesis ensuring the production of mg amount of pure and homogeneous molecules.}, keywords = {ERIANI, FRUGIER, FRUGIER IRES Integrative structural biology RNA SEC-SAXS Structure tRNA, Unité ARN}, pubstate = {published}, tppubtype = {inbook} } Over the past two decades small-angle X-ray scattering (SAXS) has become a popular method to characterize solutions of biomolecules including ribonucleic acid (RNA). In an integrative structural approach, SAXS is complementary to crystallography, NMR, and electron microscopy and provides information about RNA architecture and dynamics. This chapter highlights the practical advantages of combining size-exclusion chromatography and SAXS at synchrotron facilities. It is illustrated by practical case studies of samples ranging from single hairpins and tRNA to a large IRES. The emphasis is also put on sample preparation which is a critical step of SAXS analysis and on optimized protocols for in vitro RNA synthesis ensuring the production of mg amount of pure and homogeneous molecules. |
Riley, L G; Rudinger-Thirion, J; Frugier, M; Wilson, M; Luig, M; Alahakoon, T I; Nixon, C Y; Kirk, E P; Roscioli, T; Lunke, S; Stark, Z; Wierenga, K J; Palle, S; Walsh, M; Higgs, E; Arbuckle, S; Thirukeswaran, S; Compton, A G; Thorburn, D R; Christodoulou, J The Expanding LARS2 Phenotypic Spectrum: HLASA, Perrault Syndrome With Leukodystrophy, and Mitochondrial Myopathy Article de journal Hum Mutat, 41 (8), p. 1425-1434, 2020, ISBN: 32442335. Résumé | Liens | BibTeX | Étiquettes: ERIANI, FRUGIER, FRUGIER Perrault syndrome low frequency hearing loss primary ovarian insufficiency sensorineural hearing loss, Unité ARN @article{, title = {The Expanding LARS2 Phenotypic Spectrum: HLASA, Perrault Syndrome With Leukodystrophy, and Mitochondrial Myopathy}, author = {L G Riley and J Rudinger-Thirion and M Frugier and M Wilson and M Luig and T I Alahakoon and C Y Nixon and E P Kirk and T Roscioli and S Lunke and Z Stark and K J Wierenga and S Palle and M Walsh and E Higgs and S Arbuckle and S Thirukeswaran and A G Compton and D R Thorburn and J Christodoulou}, url = {https://pubmed.ncbi.nlm.nih.gov/32442335/?dopt=Abstract}, doi = {doi: 10.1002/humu.24050}, isbn = {32442335}, year = {2020}, date = {2020-01-01}, journal = {Hum Mutat}, volume = {41}, number = {8}, pages = {1425-1434}, abstract = {Perrault syndrome is a rare autosomal recessive disorder characterized by sensorineural hearing loss (SNHL) in both sexes and primary ovarian insufficiency in 46, XX karyotype females. Biallelic variants in five genes are reported to be causative: HSD17B4, HARS2, LARS2, CLPP and C10orf2. Here we present eight families affected by Perrault syndrome. In five families we identified novel or previously reported variants in HSD17B4, LARS2, CLPP and C10orf2. The proband from each family was whole exome sequenced and variants confirmed by Sanger sequencing. A female was compound heterozygous for a known, p.(Gly16Ser) and novel, p.(Val82Phe) variant in D-bifunctional protein (HSD17B4). A family was homozygous for mitochondrial leucyl aminocyl tRNA synthetase (mtLeuRS) (LARS2) p.(Thr522Asn), previously associated with Perrault syndrome. A further family was compound heterozygous for mtLeuRS, p.(Thr522Asn) and a novel variant, p.(Met117Ile). Affected individuals with LARS2 variants had low frequency SNHL, a feature previously described in Perrault syndrome. A female with significant neurological disability was compound heterozygous for p.(Arg323Gln) and p.(Asn399Ser) variants in Twinkle (C10orf2). A male was homozygous for a novel variant in CLPP, p.(Cys144Arg). In three families there were no putative pathogenic variants in these genes confirming additional disease-causing genes remain unidentified. We have expanded the spectrum of disease-causing variants associated with Perrault syndrome.}, keywords = {ERIANI, FRUGIER, FRUGIER Perrault syndrome low frequency hearing loss primary ovarian insufficiency sensorineural hearing loss, Unité ARN}, pubstate = {published}, tppubtype = {article} } Perrault syndrome is a rare autosomal recessive disorder characterized by sensorineural hearing loss (SNHL) in both sexes and primary ovarian insufficiency in 46, XX karyotype females. Biallelic variants in five genes are reported to be causative: HSD17B4, HARS2, LARS2, CLPP and C10orf2. Here we present eight families affected by Perrault syndrome. In five families we identified novel or previously reported variants in HSD17B4, LARS2, CLPP and C10orf2. The proband from each family was whole exome sequenced and variants confirmed by Sanger sequencing. A female was compound heterozygous for a known, p.(Gly16Ser) and novel, p.(Val82Phe) variant in D-bifunctional protein (HSD17B4). A family was homozygous for mitochondrial leucyl aminocyl tRNA synthetase (mtLeuRS) (LARS2) p.(Thr522Asn), previously associated with Perrault syndrome. A further family was compound heterozygous for mtLeuRS, p.(Thr522Asn) and a novel variant, p.(Met117Ile). Affected individuals with LARS2 variants had low frequency SNHL, a feature previously described in Perrault syndrome. A female with significant neurological disability was compound heterozygous for p.(Arg323Gln) and p.(Asn399Ser) variants in Twinkle (C10orf2). A male was homozygous for a novel variant in CLPP, p.(Cys144Arg). In three families there were no putative pathogenic variants in these genes confirming additional disease-causing genes remain unidentified. We have expanded the spectrum of disease-causing variants associated with Perrault syndrome. |
Pernod, K; Schaeffer, L; Chicher, J; Hok, E; Rick, C; Geslain, R; Eriani, G; Westhof, E; Ryckelynck, M; Martin, F The Nature of the Purine at Position 34 in tRNAs of 4-codon Boxes Is Correlated With Nucleotides at Positions 32 and 38 to Maintain Decoding Fidelity Article de journal Nucleic Acids Res, 48 (11), p. 6170-6183, 2020, ISBN: 32266934. Résumé | Liens | BibTeX | Étiquettes: ERIANI, ERIANI RYCKELYNCK WESTHOF, RYCKELYNCK, Unité ARN, WESTHOF @article{, title = {The Nature of the Purine at Position 34 in tRNAs of 4-codon Boxes Is Correlated With Nucleotides at Positions 32 and 38 to Maintain Decoding Fidelity}, author = {K Pernod and L Schaeffer and J Chicher and E Hok and C Rick and R Geslain and G Eriani and E Westhof and M Ryckelynck and F Martin}, url = {https://www.ncbi.nlm.nih.gov/pubmed/32266934?dopt=Abstract}, doi = {10.1093/nar/gkaa221}, isbn = {32266934}, year = {2020}, date = {2020-01-01}, journal = {Nucleic Acids Res}, volume = {48}, number = {11}, pages = {6170-6183}, abstract = {Translation fidelity relies essentially on the ability of ribosomes to accurately recognize triplet interactions between codons on mRNAs and anticodons of tRNAs. To determine the codon-anticodon pairs that are efficiently accepted by the eukaryotic ribosome, we took advantage of the IRES from the intergenic region (IGR) of the Cricket Paralysis Virus. It contains an essential pseudoknot PKI that structurally and functionally mimics a codon-anticodon helix. We screened the entire set of 4096 possible combinations using ultrahigh-throughput screenings combining coupled transcription/translation and droplet-based microfluidics. Only 97 combinations are efficiently accepted and accommodated for translocation and further elongation: 38 combinations involve cognate recognition with Watson-Crick pairs and 59 involve near-cognate recognition pairs with at least one mismatch. More than half of the near-cognate combinations (36/59) contain a G at the first position of the anticodon (numbered 34 of tRNA). G34-containing tRNAs decoding 4-codon boxes are almost absent from eukaryotic genomes in contrast to bacterial genomes. We reconstructed these missing tRNAs and could demonstrate that these tRNAs are toxic to cells due to their miscoding capacity in eukaryotic translation systems. We also show that the nature of the purine at position 34 is correlated with the nucleotides present at 32 and 38.}, keywords = {ERIANI, ERIANI RYCKELYNCK WESTHOF, RYCKELYNCK, Unité ARN, WESTHOF}, pubstate = {published}, tppubtype = {article} } Translation fidelity relies essentially on the ability of ribosomes to accurately recognize triplet interactions between codons on mRNAs and anticodons of tRNAs. To determine the codon-anticodon pairs that are efficiently accepted by the eukaryotic ribosome, we took advantage of the IRES from the intergenic region (IGR) of the Cricket Paralysis Virus. It contains an essential pseudoknot PKI that structurally and functionally mimics a codon-anticodon helix. We screened the entire set of 4096 possible combinations using ultrahigh-throughput screenings combining coupled transcription/translation and droplet-based microfluidics. Only 97 combinations are efficiently accepted and accommodated for translocation and further elongation: 38 combinations involve cognate recognition with Watson-Crick pairs and 59 involve near-cognate recognition pairs with at least one mismatch. More than half of the near-cognate combinations (36/59) contain a G at the first position of the anticodon (numbered 34 of tRNA). G34-containing tRNAs decoding 4-codon boxes are almost absent from eukaryotic genomes in contrast to bacterial genomes. We reconstructed these missing tRNAs and could demonstrate that these tRNAs are toxic to cells due to their miscoding capacity in eukaryotic translation systems. We also show that the nature of the purine at position 34 is correlated with the nucleotides present at 32 and 38. |
Miao, Z; Tidu, A; Eriani, G; Martin, F Secondary structure of the SARS-CoV-2 5'-UTR Article de journal RNA Biol, p. in press, 2020, ISBN: 32965173. Résumé | Liens | BibTeX | Étiquettes: ERIANI, ERIANI 5ʹ-UTR SARS-CoV-2 probing secondary structure, Unité ARN @article{, title = {Secondary structure of the SARS-CoV-2 5'-UTR}, author = {Z Miao and A Tidu and G Eriani and F Martin}, url = {https://pubmed.ncbi.nlm.nih.gov/32965173/}, doi = {10.1080/15476286.2020.1814556}, isbn = {32965173}, year = {2020}, date = {2020-01-01}, journal = {RNA Biol}, pages = {in press}, abstract = {The SARS-CoV-2, a positive-sense single-stranded RNA Coronavirus, is a global threat to human health. Thus, understanding its life cycle mechanistically would be important to facilitate the design of antiviral drugs. A key aspect of viral progression is the synthesis of viral proteins by the ribosome of the human host. In Coronaviruses, this process is regulated by the viral 5' and 3' untranslated regions (UTRs), but the precise regulatory mechanism has not yet been well understood. In particular, the 5'-UTR of the viral genome is most likely involved in translation initiation of viral proteins. Here, we performed inline probing and RNase V1 probing to establish a model of the secondary structure of SARS-CoV-2 5'-UTR. We found that the 5'-UTR contains stable structures including a very stable four-way junction close to the AUG start codon. Sequence alignment analysis of SARS-CoV-2 variants 5'-UTRs revealed a highly conserved structure with few co-variations that confirmed our secondary structure model based on probing experiments.}, keywords = {ERIANI, ERIANI 5ʹ-UTR SARS-CoV-2 probing secondary structure, Unité ARN}, pubstate = {published}, tppubtype = {article} } The SARS-CoV-2, a positive-sense single-stranded RNA Coronavirus, is a global threat to human health. Thus, understanding its life cycle mechanistically would be important to facilitate the design of antiviral drugs. A key aspect of viral progression is the synthesis of viral proteins by the ribosome of the human host. In Coronaviruses, this process is regulated by the viral 5' and 3' untranslated regions (UTRs), but the precise regulatory mechanism has not yet been well understood. In particular, the 5'-UTR of the viral genome is most likely involved in translation initiation of viral proteins. Here, we performed inline probing and RNase V1 probing to establish a model of the secondary structure of SARS-CoV-2 5'-UTR. We found that the 5'-UTR contains stable structures including a very stable four-way junction close to the AUG start codon. Sequence alignment analysis of SARS-CoV-2 variants 5'-UTRs revealed a highly conserved structure with few co-variations that confirmed our secondary structure model based on probing experiments. |
2019 |
Jackson, C B; Huemer, M; Bolognini, R; Martin, F; Szinnai, G; Donner, B C; Richter, U; Battersby, B J; Nuoffer, J M; Suomalainen, A; Schaller, A Hum Mol Genet, 28 (4), p. 639-649, 2019, ISBN: 30358850. Résumé | Liens | BibTeX | Étiquettes: ERIANI, Unité ARN @article{, title = {A variant in MRPS14 (uS14m) causes perinatal hypertrophic cardiomyopathy with neonatal lactic acidosis, growth retardation, dysmorphic features and neurological involvement}, author = {C B Jackson and M Huemer and R Bolognini and F Martin and G Szinnai and B C Donner and U Richter and B J Battersby and J M Nuoffer and A Suomalainen and A Schaller}, url = {https://www.ncbi.nlm.nih.gov/pubmed/30358850}, doi = {10.1093/hmg/ddy374}, isbn = {30358850}, year = {2019}, date = {2019-01-01}, journal = {Hum Mol Genet}, volume = {28}, number = {4}, pages = {639-649}, abstract = {Dysfunction of mitochondrial translation is increasingly an important molecular cause of human disease, but structural defects of mitochondrial ribosomal subunits are rare. We used next-generation sequencing to identify a homozygous variant in the mitochondrial small ribosomal protein 14 (MRPS14, uS14m) in a patient manifesting with perinatal hypertrophic cardiomyopathy, growth retardation, muscle hypotonia, elevated lactate, dysmorphy and mental retardation. In skeletal muscle and fibroblasts from the patient there was biochemical deficiency in complex IV of the respiratory chain. In fibroblasts mitochondrial translation was impaired and ectopic expression of a wild type MRPS14 cDNA functionally complemented this defect. Surprisingly, the mutant uS14m was stable and did not affect assembly of the small ribosomal subunit. Instead, structural modeling of the uS14m mutation predicted a disruption to the ribosomal mRNA channel. Collectively, our data demonstrates pathogenic mutations in MRPS14 can manifest as a perinatal-onset mitochondrial hypertrophic cardiomyopathy with a novel molecular pathogenic mechanism that impairs the function of mitochondrial ribosomes during translation elongation or mitochondrial mRNA recruitment rather than assembly.}, keywords = {ERIANI, Unité ARN}, pubstate = {published}, tppubtype = {article} } Dysfunction of mitochondrial translation is increasingly an important molecular cause of human disease, but structural defects of mitochondrial ribosomal subunits are rare. We used next-generation sequencing to identify a homozygous variant in the mitochondrial small ribosomal protein 14 (MRPS14, uS14m) in a patient manifesting with perinatal hypertrophic cardiomyopathy, growth retardation, muscle hypotonia, elevated lactate, dysmorphy and mental retardation. In skeletal muscle and fibroblasts from the patient there was biochemical deficiency in complex IV of the respiratory chain. In fibroblasts mitochondrial translation was impaired and ectopic expression of a wild type MRPS14 cDNA functionally complemented this defect. Surprisingly, the mutant uS14m was stable and did not affect assembly of the small ribosomal subunit. Instead, structural modeling of the uS14m mutation predicted a disruption to the ribosomal mRNA channel. Collectively, our data demonstrates pathogenic mutations in MRPS14 can manifest as a perinatal-onset mitochondrial hypertrophic cardiomyopathy with a novel molecular pathogenic mechanism that impairs the function of mitochondrial ribosomes during translation elongation or mitochondrial mRNA recruitment rather than assembly. |
van der Knaap, M S; Bugiani, M; Mendes, M I; Riley, L G; Smith, D E C; Rudinger-Thirion, J; Frugier, M; Breur, M; Crawford, J; van Gaalen, J; Schouten, M; Willems, M; Waisfisz, Q; Mau-Them, F T; Rodenburg, R J; Taft, R J; Keren, B; Christodoulou, J; Depienne, C; Simons, C; Salomons, G S; Mochel, F Biallelic variants in LARS2 and KARS cause deafness and (ovario)leukodystrophy Article de journal Neurology, 92 (11), p. e1225-e1237, 2019, ISBN: 30737337. Résumé | Liens | BibTeX | Étiquettes: ERIANI, FRUGIER, Unité ARN @article{, title = {Biallelic variants in \textit{LARS2} and \textit{KARS} cause deafness and (ovario)leukodystrophy}, author = {M S van der Knaap and M Bugiani and M I Mendes and L G Riley and D E C Smith and J Rudinger-Thirion and M Frugier and M Breur and J Crawford and J van Gaalen and M Schouten and M Willems and Q Waisfisz and F T Mau-Them and R J Rodenburg and R J Taft and B Keren and J Christodoulou and C Depienne and C Simons and G S Salomons and F Mochel}, url = {https://www.ncbi.nlm.nih.gov/pubmed/30737337}, doi = {10.1212/WNL.0000000000007098}, isbn = {30737337}, year = {2019}, date = {2019-01-01}, journal = {Neurology}, volume = {92}, number = {11}, pages = {e1225-e1237}, abstract = {OBJECTIVE: To describe the leukodystrophy caused by pathogenic variants in LARS2 and KARS, encoding mitochondrial leucyl transfer RNA (tRNA) synthase and mitochondrial and cytoplasmic lysyl tRNA synthase, respectively. METHODS: We composed a group of 5 patients with leukodystrophy, in whom whole-genome or whole-exome sequencing revealed pathogenic variants in LARS2 or KARS. Clinical information, brain MRIs, and postmortem brain autopsy data were collected. We assessed aminoacylation activities of purified mutant recombinant mitochondrial leucyl tRNA synthase and performed aminoacylation assays on patients' lymphoblasts and fibroblasts. RESULTS: Patients had a combination of early-onset deafness and later-onset neurologic deterioration caused by progressive brain white matter abnormalities on MRI. Female patients with LARS2 pathogenic variants had premature ovarian failure. In 2 patients, MRI showed additional signs of early-onset vascular abnormalities. In 2 other patients with LARS2 and KARS pathogenic variants, magnetic resonance spectroscopy revealed elevated white matter lactate, suggesting mitochondrial disease. Pathology in one patient with LARS2 pathogenic variants displayed evidence of primary disease of oligodendrocytes and astrocytes with lack of myelin and deficient astrogliosis. Aminoacylation activities of purified recombinant mutant leucyl tRNA synthase showed a 3-fold loss of catalytic efficiency. Aminoacylation assays on patients' lymphoblasts and fibroblasts showed about 50% reduction of enzyme activity. CONCLUSION: This study adds LARS2 and KARS pathogenic variants as gene defects that may underlie deafness, ovarian failure, and leukodystrophy with mitochondrial signature. We discuss the specific MRI characteristics shared by leukodystrophies caused by mitochondrial tRNA synthase defects. We propose to add aminoacylation assays as biochemical diagnostic tools for leukodystrophies.}, keywords = {ERIANI, FRUGIER, Unité ARN}, pubstate = {published}, tppubtype = {article} } OBJECTIVE: To describe the leukodystrophy caused by pathogenic variants in LARS2 and KARS, encoding mitochondrial leucyl transfer RNA (tRNA) synthase and mitochondrial and cytoplasmic lysyl tRNA synthase, respectively. METHODS: We composed a group of 5 patients with leukodystrophy, in whom whole-genome or whole-exome sequencing revealed pathogenic variants in LARS2 or KARS. Clinical information, brain MRIs, and postmortem brain autopsy data were collected. We assessed aminoacylation activities of purified mutant recombinant mitochondrial leucyl tRNA synthase and performed aminoacylation assays on patients' lymphoblasts and fibroblasts. RESULTS: Patients had a combination of early-onset deafness and later-onset neurologic deterioration caused by progressive brain white matter abnormalities on MRI. Female patients with LARS2 pathogenic variants had premature ovarian failure. In 2 patients, MRI showed additional signs of early-onset vascular abnormalities. In 2 other patients with LARS2 and KARS pathogenic variants, magnetic resonance spectroscopy revealed elevated white matter lactate, suggesting mitochondrial disease. Pathology in one patient with LARS2 pathogenic variants displayed evidence of primary disease of oligodendrocytes and astrocytes with lack of myelin and deficient astrogliosis. Aminoacylation activities of purified recombinant mutant leucyl tRNA synthase showed a 3-fold loss of catalytic efficiency. Aminoacylation assays on patients' lymphoblasts and fibroblasts showed about 50% reduction of enzyme activity. CONCLUSION: This study adds LARS2 and KARS pathogenic variants as gene defects that may underlie deafness, ovarian failure, and leukodystrophy with mitochondrial signature. We discuss the specific MRI characteristics shared by leukodystrophies caused by mitochondrial tRNA synthase defects. We propose to add aminoacylation assays as biochemical diagnostic tools for leukodystrophies. |
Janvier, A; Despons, L; Schaeffer, L; Tidu, A; Martin, F; Eriani, G A tRNA-mimic Strategy to Explore the Role of G34 of tRNAGly in Translation and Codon Frameshifting Article de journal Int J Mol Sci, 20 (16), p. 3911, 2019, ISBN: 31405256. Résumé | Liens | BibTeX | Étiquettes: ERIANI, ERIANI LESCURE IRES element frameshifting genetic code glycine codon tRNA translation, Unité ARN @article{, title = {A tRNA-mimic Strategy to Explore the Role of G34 of tRNA^{Gly} in Translation and Codon Frameshifting}, author = {A Janvier and L Despons and L Schaeffer and A Tidu and F Martin and G Eriani}, url = {https://www.ncbi.nlm.nih.gov/pubmed/31405256?dopt=Abstract}, doi = {10.3390/ijms20163911}, isbn = {31405256}, year = {2019}, date = {2019-01-01}, journal = {Int J Mol Sci}, volume = {20}, number = {16}, pages = {3911}, abstract = {Decoding of the 61 sense codons of the genetic code requires a variable number of tRNAs that establish codon-anticodon interactions. Thanks to the wobble base pairing at the third codon position, less than 61 different tRNA isoacceptors are needed to decode the whole set of codons. On the tRNA, a subtle distribution of nucleoside modifications shapes the anticodon loop structure and participates to accurate decoding and reading frame maintenance. Interestingly, although the 61 anticodons should exist in tRNAs, a strict absence of some tRNAs decoders is found in several codon families. For instance, in Eukaryotes, G34-containing tRNAs translating 3-, 4- and 6-codon boxes are absent. This includes tRNA specific for Ala, Arg, Ile, Leu, Pro, Ser, Thr, and Val. tRNAGly is the only exception for which in the three kingdoms, a G34-containing tRNA exists to decode C3 and U3-ending codons. To understand why G34-tRNAGly exists, we analysed at the genome wide level the codon distribution in codon +1 relative to the four GGN Gly codons. When considering codon GGU, a bias was found towards an unusual high usage of codons starting with a G whatever the amino acid at +1 codon. It is expected that GGU codons are decoded by G34-containing tRNAGly, decoding also GGC codons. Translation studies revealed that the presence of a G at the first position of the downstream codon reduces the +1 frameshift by stabilizing the G34U3 wobble interaction. This result partially explains why G34-containing tRNAGly exists in Eukaryotes whereas all the other G34-containing tRNAs for multiple codon boxes are absent.}, keywords = {ERIANI, ERIANI LESCURE IRES element frameshifting genetic code glycine codon tRNA translation, Unité ARN}, pubstate = {published}, tppubtype = {article} } Decoding of the 61 sense codons of the genetic code requires a variable number of tRNAs that establish codon-anticodon interactions. Thanks to the wobble base pairing at the third codon position, less than 61 different tRNA isoacceptors are needed to decode the whole set of codons. On the tRNA, a subtle distribution of nucleoside modifications shapes the anticodon loop structure and participates to accurate decoding and reading frame maintenance. Interestingly, although the 61 anticodons should exist in tRNAs, a strict absence of some tRNAs decoders is found in several codon families. For instance, in Eukaryotes, G34-containing tRNAs translating 3-, 4- and 6-codon boxes are absent. This includes tRNA specific for Ala, Arg, Ile, Leu, Pro, Ser, Thr, and Val. tRNAGly is the only exception for which in the three kingdoms, a G34-containing tRNA exists to decode C3 and U3-ending codons. To understand why G34-tRNAGly exists, we analysed at the genome wide level the codon distribution in codon +1 relative to the four GGN Gly codons. When considering codon GGU, a bias was found towards an unusual high usage of codons starting with a G whatever the amino acid at +1 codon. It is expected that GGU codons are decoded by G34-containing tRNAGly, decoding also GGC codons. Translation studies revealed that the presence of a G at the first position of the downstream codon reduces the +1 frameshift by stabilizing the G34U3 wobble interaction. This result partially explains why G34-containing tRNAGly exists in Eukaryotes whereas all the other G34-containing tRNAs for multiple codon boxes are absent. |
2018 |
Tabet, R; Schaeffer, L; Freyermuth, F; Jambeau, M; Workman, M; Lee, C Z; Lin, C C; Jiang, J; Jansen-West, K; Abou-Hamdan, H; Désaubry, L; Gendron, T; Petrucelli, L; Martin, F; Lagier-Tourenne, C CUG initiation and frameshifting enable production of dipeptide repeat proteins from ALS/FTD C9ORF72 transcript Article de journal Nat Commun, 9 (1), p. 152, 2018, ISBN: 29323119. Résumé | Liens | BibTeX | Étiquettes: ERIANI, Unité ARN @article{, title = {CUG initiation and frameshifting enable production of dipeptide repeat proteins from ALS/FTD C9ORF72 transcript}, author = {R Tabet and L Schaeffer and F Freyermuth and M Jambeau and M Workman and C Z Lee and C C Lin and J Jiang and K Jansen-West and H Abou-Hamdan and L Désaubry and T Gendron and L Petrucelli and F Martin and C Lagier-Tourenne}, url = {https://www.ncbi.nlm.nih.gov/pubmed/29323119?dopt=Abstract}, doi = {10.1038/s41467-017-02643-5}, isbn = {29323119}, year = {2018}, date = {2018-01-01}, journal = {Nat Commun}, volume = {9}, number = {1}, pages = {152}, abstract = {Expansion of G4C2 repeats in the C9ORF72 gene is the most prevalent inherited form of amyotrophic lateral sclerosis and frontotemporal dementia. Expanded transcripts undergo repeat-associated non-AUG (RAN) translation producing dipeptide repeat proteins from all reading frames. We determined cis-factors and trans-factors influencing translation of the human C9ORF72 transcripts. G4C2 translation operates through a 5'-3' cap-dependent scanning mechanism, requiring a CUG codon located upstream of the repeats and an initiator Met-tRNAMeti. Production of poly-GA, poly-GP, and poly-GR proteins from the three frames is influenced by mutation of the same CUG start codon supporting a frameshifting mechanism. RAN translation is also regulated by an upstream open reading frame (uORF) present in mis-spliced C9ORF72 transcripts. Inhibitors of the pre-initiation ribosomal complex and RNA antisense oligonucleotides selectively targeting the 5'-flanking G4C2 sequence block ribosomal scanning and prevent translation. Finally, we identified an unexpected affinity of expanded transcripts for the ribosomal subunits independently from translation.}, keywords = {ERIANI, Unité ARN}, pubstate = {published}, tppubtype = {article} } Expansion of G4C2 repeats in the C9ORF72 gene is the most prevalent inherited form of amyotrophic lateral sclerosis and frontotemporal dementia. Expanded transcripts undergo repeat-associated non-AUG (RAN) translation producing dipeptide repeat proteins from all reading frames. We determined cis-factors and trans-factors influencing translation of the human C9ORF72 transcripts. G4C2 translation operates through a 5'-3' cap-dependent scanning mechanism, requiring a CUG codon located upstream of the repeats and an initiator Met-tRNAMeti. Production of poly-GA, poly-GP, and poly-GR proteins from the three frames is influenced by mutation of the same CUG start codon supporting a frameshifting mechanism. RAN translation is also regulated by an upstream open reading frame (uORF) present in mis-spliced C9ORF72 transcripts. Inhibitors of the pre-initiation ribosomal complex and RNA antisense oligonucleotides selectively targeting the 5'-flanking G4C2 sequence block ribosomal scanning and prevent translation. Finally, we identified an unexpected affinity of expanded transcripts for the ribosomal subunits independently from translation. |
Mailliot, J; Martin, F Viral internal ribosomal entry sites: four classes for one goal Article de journal Wiley Interdiscip Rev RNA, 9 (2), p. none, 2018, ISBN: 29193740. Résumé | Liens | BibTeX | Étiquettes: ERIANI, Unité ARN @article{, title = {Viral internal ribosomal entry sites: four classes for one goal}, author = {J Mailliot and F Martin}, url = {https://www.ncbi.nlm.nih.gov/pubmed/29193740?dopt=Abstract}, doi = {10.1002/wrna.1458}, isbn = {29193740}, year = {2018}, date = {2018-01-01}, journal = {Wiley Interdiscip Rev RNA}, volume = {9}, number = {2}, pages = {none}, abstract = {To ensure efficient propagation, viruses need to rapidly produce viral proteins after cell entrance. Since viral genomes do not encode any components of the protein biosynthesis machinery, viral proteins must be produced by the host cell. To hi-jack the host cellular translation, viruses use a great variety of distinct strategies. Many single-stranded positive-sensed RNA viruses contain so-called internal ribosome entry sites (IRESs). IRESs are structural RNA motifs that have evolved to specific folds that recruit the host ribosomes on the viral coding sequences in order to synthesize viral proteins. In host canonical translation, recruitment of the translation machinery components is essentially guided by the 5' cap (m7 G) of mRNA. In contrast, IRESs are able to promote efficient ribosome assembly internally and in cap-independent manner. IRESs have been categorized into four classes, based on their length, nucleotide sequence, secondary and tertiary structures, as well as their mode of action. Classes I and II require the assistance of cellular auxiliary factors, the eukaryotic intiation factors (eIF), for efficient ribosome assembly. Class III IRESs require only a subset of eIFs whereas Class IV, which are the more compact, can promote translation without any eIFs. Extensive functional and structural investigations of IRESs over the past decades have allowed a better understanding of their mode of action for viral translation. Because viral translation has a pivotal role in the infectious program, IRESs are therefore attractive targets for therapeutic purposes. For further resources related to this article, please visit the WIREs website.}, keywords = {ERIANI, Unité ARN}, pubstate = {published}, tppubtype = {article} } To ensure efficient propagation, viruses need to rapidly produce viral proteins after cell entrance. Since viral genomes do not encode any components of the protein biosynthesis machinery, viral proteins must be produced by the host cell. To hi-jack the host cellular translation, viruses use a great variety of distinct strategies. Many single-stranded positive-sensed RNA viruses contain so-called internal ribosome entry sites (IRESs). IRESs are structural RNA motifs that have evolved to specific folds that recruit the host ribosomes on the viral coding sequences in order to synthesize viral proteins. In host canonical translation, recruitment of the translation machinery components is essentially guided by the 5' cap (m7 G) of mRNA. In contrast, IRESs are able to promote efficient ribosome assembly internally and in cap-independent manner. IRESs have been categorized into four classes, based on their length, nucleotide sequence, secondary and tertiary structures, as well as their mode of action. Classes I and II require the assistance of cellular auxiliary factors, the eukaryotic intiation factors (eIF), for efficient ribosome assembly. Class III IRESs require only a subset of eIFs whereas Class IV, which are the more compact, can promote translation without any eIFs. Extensive functional and structural investigations of IRESs over the past decades have allowed a better understanding of their mode of action for viral translation. Because viral translation has a pivotal role in the infectious program, IRESs are therefore attractive targets for therapeutic purposes. For further resources related to this article, please visit the WIREs website. |
Riley, L G; Heeney, M M; Rudinger-Thirion, J; Frugier, M; Campagna, D R; Zhou, R; Hale, G A; Hilliard, L M; Kaplan, J A; Kwiatkowski, J L; Sieff, C A; Steensma, D P; Rennings, A J; Simons, A; Schaap, N; Roodenburg, R J; Kleefstra, T; Arenillas, L; Fita-Torró, J; Ahmed, R; Abboud, M; Bechara, E; Farah, R; Tamminga, R Y; Bottomley, S S; Sanchez, M; Swinkels, D W; Christodoulou, J; Fleming, M D The phenotypic spectrum of germline YARS2 variants: from isolated sideroblastic anemia to mitochondrial myopathy, lactic acidosis and sideroblastic anemia 2 Article de journal Haematologica, 103 (12), p. 2008-2015, 2018, ISBN: 30026338. Résumé | Liens | BibTeX | Étiquettes: ERIANI, FRUGIER, FRUGIER Congenital sideroblastic anemia MLASA YARS2 mitochondrial myopathy sideroblastic anemia, Unité ARN @article{, title = {The phenotypic spectrum of germline YARS2 variants: from isolated sideroblastic anemia to mitochondrial myopathy, lactic acidosis and sideroblastic anemia 2}, author = {L G Riley and M M Heeney and J Rudinger-Thirion and M Frugier and D R Campagna and R Zhou and G A Hale and L M Hilliard and J A Kaplan and J L Kwiatkowski and C A Sieff and D P Steensma and A J Rennings and A Simons and N Schaap and R J Roodenburg and T Kleefstra and L Arenillas and J Fita-Torró and R Ahmed and M Abboud and E Bechara and R Farah and R Y Tamminga and S S Bottomley and M Sanchez and D W Swinkels and J Christodoulou and M D Fleming}, url = {https://www.ncbi.nlm.nih.gov/pubmed/30026338}, doi = {10.3324/haematol.2017.182659}, isbn = {30026338}, year = {2018}, date = {2018-01-01}, journal = {Haematologica}, volume = {103}, number = {12}, pages = {2008-2015}, abstract = {YARS2 variants have previously been described in patients with myopathy, lactic acidosis and sideroblastic anemia 2 (MLASA2). YARS2 encodes the mitochondrial tyrosyl-tRNA synthetase, which is responsible for conjugating tyrosine to its cognate mt-tRNA for mitochondrial protein synthesis. Here we describe 14 individuals from 11 families presenting with sideroblastic anemia and with YARS2 variants that we identified using a sideroblastic anemia gene panel or exome sequencing. The phenotype of these patients ranged from MLASA to isolated congenital sideroblastic anemia. As in previous cases, inter- and intra-familial phenotypic variability was observed, however this report includes the first cases with isolated sideroblastic anemia and patients with biallelic YARS2 variants that have no clinically ascertainable phenotype. We identified ten novel YARS2 variants and three previously reported variants. In vitro amino-acylation assays of three five novel missense variants showed they that three had less effect on the catalytic activity of YARS2 than the most commonly reported variant, p.(Phe52Leu), associated with MLASA2, which may explain the milder phenotypes in patients with these variants. However, the other two missense variants had a more severe effect on YARS2 catalytic efficiency. Several patients carried the common YARS2 c.572 G>T, p.(Gly191Val) variant (minor allele frequency = 0.1259) in trans with a rare deleterious YARS2 variant. We have previously shown that the p.(Gly191Val) variant reduces YARS2 catalytic activity. Consequently, we suggest that biallelic YARS2 variants, including severe loss-of-function alleles in trans of the common p.(Gly191Val) variant, should be considered as a cause of isolated congenital sideroblastic anemia, as well as the MLASA syndromic phenotype.}, keywords = {ERIANI, FRUGIER, FRUGIER Congenital sideroblastic anemia MLASA YARS2 mitochondrial myopathy sideroblastic anemia, Unité ARN}, pubstate = {published}, tppubtype = {article} } YARS2 variants have previously been described in patients with myopathy, lactic acidosis and sideroblastic anemia 2 (MLASA2). YARS2 encodes the mitochondrial tyrosyl-tRNA synthetase, which is responsible for conjugating tyrosine to its cognate mt-tRNA for mitochondrial protein synthesis. Here we describe 14 individuals from 11 families presenting with sideroblastic anemia and with YARS2 variants that we identified using a sideroblastic anemia gene panel or exome sequencing. The phenotype of these patients ranged from MLASA to isolated congenital sideroblastic anemia. As in previous cases, inter- and intra-familial phenotypic variability was observed, however this report includes the first cases with isolated sideroblastic anemia and patients with biallelic YARS2 variants that have no clinically ascertainable phenotype. We identified ten novel YARS2 variants and three previously reported variants. In vitro amino-acylation assays of three five novel missense variants showed they that three had less effect on the catalytic activity of YARS2 than the most commonly reported variant, p.(Phe52Leu), associated with MLASA2, which may explain the milder phenotypes in patients with these variants. However, the other two missense variants had a more severe effect on YARS2 catalytic efficiency. Several patients carried the common YARS2 c.572 G>T, p.(Gly191Val) variant (minor allele frequency = 0.1259) in trans with a rare deleterious YARS2 variant. We have previously shown that the p.(Gly191Val) variant reduces YARS2 catalytic activity. Consequently, we suggest that biallelic YARS2 variants, including severe loss-of-function alleles in trans of the common p.(Gly191Val) variant, should be considered as a cause of isolated congenital sideroblastic anemia, as well as the MLASA syndromic phenotype. |
Cela, M; Paulus, C; Santos, M A S; Moura, G R; Frugier, M; Rudinger-Thirion, J Plasmodium apicoplast tyrosyl-tRNA synthetase recognizes an unusual, simplified identity set in cognate tRNATyr Article de journal PLoS One, 13 (12), p. e0209805, 2018, ISBN: 30592748. Résumé | Liens | BibTeX | Étiquettes: ERIANI, FRUGIER, Unité ARN @article{, title = {Plasmodium apicoplast tyrosyl-tRNA synthetase recognizes an unusual, simplified identity set in cognate tRNATyr}, author = {M Cela and C Paulus and M A S Santos and G R Moura and M Frugier and J Rudinger-Thirion}, url = {https://www.ncbi.nlm.nih.gov/pubmed/30592748?dopt=Abstract}, doi = {10.1371/journal.pone.0209805}, isbn = {30592748}, year = {2018}, date = {2018-01-01}, journal = {PLoS One}, volume = {13}, number = {12}, pages = {e0209805}, abstract = {The life cycle of Plasmodium falciparum, the agent responsible for malaria, depends on both cytosolic and apicoplast translation fidelity. Apicoplast aminoacyl-tRNA synthetases (aaRS) are bacterial-like enzymes devoted to organellar tRNA aminoacylation. They are all encoded by the nuclear genome and are translocated into the apicoplast only after cytosolic biosynthesis. Apicoplast aaRSs contain numerous idiosyncratic sequence insertions: An understanding of the roles of these insertions has remained elusive and they hinder efforts to heterologously overexpress these proteins. Moreover, the A/T rich content of the Plasmodium genome leads to A/U rich apicoplast tRNA substrates that display structural plasticity. Here, we focus on the P. falciparum apicoplast tyrosyl-tRNA synthetase (Pf-apiTyrRS) and its cognate tRNATyr substrate (Pf-apitRNATyr). Cloning and expression strategies used to obtain an active and functional recombinant Pf-apiTyrRS are reported. Functional analyses established that only three weak identity elements in the apitRNATyr promote specific recognition by the cognate Pf-apiTyrRS and that positive identity elements usually found in the tRNATyr acceptor stem are excluded from this set. This finding brings to light an unusual behavior for a tRNATyr aminoacylation system and suggests that Pf-apiTyrRS uses primarily negative recognition elements to direct tyrosylation specificity.}, keywords = {ERIANI, FRUGIER, Unité ARN}, pubstate = {published}, tppubtype = {article} } The life cycle of Plasmodium falciparum, the agent responsible for malaria, depends on both cytosolic and apicoplast translation fidelity. Apicoplast aminoacyl-tRNA synthetases (aaRS) are bacterial-like enzymes devoted to organellar tRNA aminoacylation. They are all encoded by the nuclear genome and are translocated into the apicoplast only after cytosolic biosynthesis. Apicoplast aaRSs contain numerous idiosyncratic sequence insertions: An understanding of the roles of these insertions has remained elusive and they hinder efforts to heterologously overexpress these proteins. Moreover, the A/T rich content of the Plasmodium genome leads to A/U rich apicoplast tRNA substrates that display structural plasticity. Here, we focus on the P. falciparum apicoplast tyrosyl-tRNA synthetase (Pf-apiTyrRS) and its cognate tRNATyr substrate (Pf-apitRNATyr). Cloning and expression strategies used to obtain an active and functional recombinant Pf-apiTyrRS are reported. Functional analyses established that only three weak identity elements in the apitRNATyr promote specific recognition by the cognate Pf-apiTyrRS and that positive identity elements usually found in the tRNATyr acceptor stem are excluded from this set. This finding brings to light an unusual behavior for a tRNATyr aminoacylation system and suggests that Pf-apiTyrRS uses primarily negative recognition elements to direct tyrosylation specificity. |
Gross, L; Schaeffer, L; Alghoul, F; Hayek, H; Allmang, C; Eriani, G; Martin, F Tracking the m7G-cap during translation initiation by crosslinking methods Article de journal Methods, 137 , p. 3-10, 2018, ISBN: 29307728. Résumé | Liens | BibTeX | Étiquettes: ERIANI, ERIANI Cap-dependent translation Chemical crosslinking Histone H4 mRNA Ribosome UV crosslinking eIF4E, Unité ARN @article{, title = {Tracking the m^{7}G-cap during translation initiation by crosslinking methods}, author = {L Gross and L Schaeffer and F Alghoul and H Hayek and C Allmang and G Eriani and F Martin}, url = {https://www.ncbi.nlm.nih.gov/pubmed/29307728?dopt=Abstract}, doi = {10.1016/j.ymeth.2017.12.019}, isbn = {29307728}, year = {2018}, date = {2018-01-01}, journal = {Methods}, volume = {137}, pages = {3-10}, abstract = {In eukaryotes, cap-dependent translation initiation is a sophisticated process that requires numerous trans-acting factors, the eukaryotic Initiation Factors (eIFs). Their main function is to assist the ribosome for accurate AUG start codon recognition. The whole process requires a 5'-3' scanning step and is therefore highly dynamic. Therefore translation requires a complex interplay between eIFs through assembly/release cycles. Here, we describe an original approach to assess the dynamic features of translation initiation. The principle is to use the m7Gcap located at the 5' extremity of mRNAs as a tracker to monitor RNA and protein components that are in its vicinity. Cap-binding molecules are trapped by chemical and UV crosslinking. The combination of cap crosslinking methods in cell-free translation systems with the use of specific translation inhibitors for different steps such as edeine, GMP-PNP or cycloheximide allowed assessing the cap fate during eukaryotic translation. Here, we followed the position of the cap in the histone H4 mRNA and the cap binding proteins during H4 mRNA translation.}, keywords = {ERIANI, ERIANI Cap-dependent translation Chemical crosslinking Histone H4 mRNA Ribosome UV crosslinking eIF4E, Unité ARN}, pubstate = {published}, tppubtype = {article} } In eukaryotes, cap-dependent translation initiation is a sophisticated process that requires numerous trans-acting factors, the eukaryotic Initiation Factors (eIFs). Their main function is to assist the ribosome for accurate AUG start codon recognition. The whole process requires a 5'-3' scanning step and is therefore highly dynamic. Therefore translation requires a complex interplay between eIFs through assembly/release cycles. Here, we describe an original approach to assess the dynamic features of translation initiation. The principle is to use the m7Gcap located at the 5' extremity of mRNAs as a tracker to monitor RNA and protein components that are in its vicinity. Cap-binding molecules are trapped by chemical and UV crosslinking. The combination of cap crosslinking methods in cell-free translation systems with the use of specific translation inhibitors for different steps such as edeine, GMP-PNP or cycloheximide allowed assessing the cap fate during eukaryotic translation. Here, we followed the position of the cap in the histone H4 mRNA and the cap binding proteins during H4 mRNA translation. |
Gribling-Burrer, A S; Eriani, G; Allmang, C Modification of Selenoprotein mRNAs by Cap Tri-methylation Book Chapter Chavatte, L (Ed.): Selenoproteins: Methods and Protocols, 1661 , p. 125-141, Springer Protocols, Humana Press, 2018, ISBN: 28917041. Résumé | Liens | BibTeX | Étiquettes: 2, 7G cap, ERIANI, ERIANI Cap hypermethylation Cap immunoprecipitation Selenoprotein mRNAs TMG cap Tgs1 m3 2, Unité ARN @inbook{, title = {Modification of Selenoprotein mRNAs by Cap Tri-methylation}, author = {A S Gribling-Burrer and G Eriani and C Allmang}, editor = {L Chavatte}, url = {https://www.ncbi.nlm.nih.gov/pubmed/28917041?dopt=Abstract}, doi = {1007/978-1-4939-7258-6_9}, isbn = {28917041}, year = {2018}, date = {2018-01-01}, booktitle = {Selenoproteins: Methods and Protocols}, volume = {1661}, pages = {125-141}, publisher = {Springer Protocols, Humana Press}, series = {Methods in Molecular Biology}, abstract = {Several selenoprotein mRNAs undergo 5' cap maturation events whereby their classical monomethylated m7G cap becomes trimethylated (m32,2,7G) by the trimethylguanosine synthase 1 (Tgs1). Here, we describe immunoprecipitation methods for the detection of endogenous m32,2,7G-capped selenoprotein mRNAs from total cell extracts or after polysome fractionation of cytoplasmic extracts. We have also developed a method for the in vitro cap hypermethylation of selenoprotein mRNA transcripts using purified Tgs1 enzyme.}, keywords = {2, 7G cap, ERIANI, ERIANI Cap hypermethylation Cap immunoprecipitation Selenoprotein mRNAs TMG cap Tgs1 m3 2, Unité ARN}, pubstate = {published}, tppubtype = {inbook} } Several selenoprotein mRNAs undergo 5' cap maturation events whereby their classical monomethylated m7G cap becomes trimethylated (m32,2,7G) by the trimethylguanosine synthase 1 (Tgs1). Here, we describe immunoprecipitation methods for the detection of endogenous m32,2,7G-capped selenoprotein mRNAs from total cell extracts or after polysome fractionation of cytoplasmic extracts. We have also developed a method for the in vitro cap hypermethylation of selenoprotein mRNA transcripts using purified Tgs1 enzyme. |
Eriani, G; Martin, F START: STructure-Assisted RNA Translation Article de journal RNA Biol, 15 (9), p. 1250-1253, 2018, ISBN: 30176155. Résumé | Liens | BibTeX | Étiquettes: ERIANI, ERIANI Ded1/DDX3 RNA helicase Ribosome Scanning Translation initiation messenger RNA, Unité ARN @article{, title = {START: STructure-Assisted RNA Translation}, author = {G Eriani and F Martin}, url = {https://www.ncbi.nlm.nih.gov/pubmed/30176155?dopt=Abstract}, doi = {10.1080/15476286.2018.1518855}, isbn = {30176155}, year = {2018}, date = {2018-01-01}, journal = {RNA Biol}, volume = {15}, number = {9}, pages = {1250-1253}, abstract = {Cap-dependent translation initiation begins by assembly of a pre-initiation ribosomal complex that scans the 5' Untranslated Region in order to localise the start codon. During this process, RNA secondary structures are melted by RNA helicases. Guenther et al reported that the yeast helicase Ded1, an orthologue of the mammalian DDX3 helicase, is responsible for this activity. When Ded1 is non-functional, RNA structures in the 5'UTR promote translation initiation on Alternative Translation Initiation Sites (ATIS) lead to uORF translation and consequently down-regulation of the main ORF. This mechanism is driven by the sole presence of RNA secondary structures located downstream of ATIS. Translation initiation mediated by RNA structures is found in other messenger RNAs. We propose to name this novel mechanism STructure-Assisted-RNA-Translation or START.}, keywords = {ERIANI, ERIANI Ded1/DDX3 RNA helicase Ribosome Scanning Translation initiation messenger RNA, Unité ARN}, pubstate = {published}, tppubtype = {article} } Cap-dependent translation initiation begins by assembly of a pre-initiation ribosomal complex that scans the 5' Untranslated Region in order to localise the start codon. During this process, RNA secondary structures are melted by RNA helicases. Guenther et al reported that the yeast helicase Ded1, an orthologue of the mammalian DDX3 helicase, is responsible for this activity. When Ded1 is non-functional, RNA structures in the 5'UTR promote translation initiation on Alternative Translation Initiation Sites (ATIS) lead to uORF translation and consequently down-regulation of the main ORF. This mechanism is driven by the sole presence of RNA secondary structures located downstream of ATIS. Translation initiation mediated by RNA structures is found in other messenger RNAs. We propose to name this novel mechanism STructure-Assisted-RNA-Translation or START. |
2017 |
Kobeissy, F; Shaito, A; Kaplan, A; Baki, L; Hayek, H; Dagher-Hamalian, C; Nehme, A; Ghali, R; Abidi, E; Husari, A; Zeidan, A; Zouein, F A; Zibara, K Acute Exposure to Cigarette Smoking Followed by Myocardial Infarction Aggravates Renal Damage in an In Vivo Mouse Model. Article de journal Oxid Med Cell Longev, 2017 , p. 5135241, 2017, ISBN: 29177025. Résumé | Liens | BibTeX | Étiquettes: ERIANI, Unité ARN @article{, title = {Acute Exposure to Cigarette Smoking Followed by Myocardial Infarction Aggravates Renal Damage in an \textit{In Vivo} Mouse Model.}, author = {F Kobeissy and A Shaito and A Kaplan and L Baki and H Hayek and C Dagher-Hamalian and A Nehme and R Ghali and E Abidi and A Husari and A Zeidan and F A Zouein and K Zibara}, url = {https://www.ncbi.nlm.nih.gov/pubmed/29177025?dopt=Abstract}, doi = {10.1155/2017/5135241}, isbn = {29177025}, year = {2017}, date = {2017-01-01}, journal = {Oxid Med Cell Longev}, volume = {2017}, pages = {5135241}, abstract = {Cigarette smoking (S) is a risk factor for progressive chronic kidney disease, renal dysfunction, and renal failure. In this study, the effect of smoking on kidney function was investigated in a mouse model of myocardial infarction (MI) using 4 groups: control (C), smoking (S), MI, and S+MI. Histological analysis of S+MI group showed alterations in kidney structure including swelling of the proximal convoluted tubules (PCTs), thinning of the epithelial lining, focal loss of the brush border of PCTs, and patchy glomerular retraction. Molecular analysis revealed that nephrin expression was significantly reduced in the S+MI group, whereas sodium-hydrogen exchanger-1 (NHE-1) was significantly increased, suggesting altered glomerular filtration and kidney functions. Moreover, S+MI group, but not S alone, showed a significant increase in the expression of connective tissue growth factor (CTGF) and fibrotic proteins fibronectin (FN) and α-smooth muscle actin (SMA), in comparison to controls, in addition to a significant increase in mRNA levels of IL-6 and TNF-α inflammatory markers. Finally, reactive oxygen species (ROS) production was significantly accentuated in S+MI group concomitant with a significant increase in NOX-4 protein levels. In conclusion, smoking aggravates murine acute renal damage caused by MI at the structural and molecular levels by exacerbating renal dysfunction.}, keywords = {ERIANI, Unité ARN}, pubstate = {published}, tppubtype = {article} } Cigarette smoking (S) is a risk factor for progressive chronic kidney disease, renal dysfunction, and renal failure. In this study, the effect of smoking on kidney function was investigated in a mouse model of myocardial infarction (MI) using 4 groups: control (C), smoking (S), MI, and S+MI. Histological analysis of S+MI group showed alterations in kidney structure including swelling of the proximal convoluted tubules (PCTs), thinning of the epithelial lining, focal loss of the brush border of PCTs, and patchy glomerular retraction. Molecular analysis revealed that nephrin expression was significantly reduced in the S+MI group, whereas sodium-hydrogen exchanger-1 (NHE-1) was significantly increased, suggesting altered glomerular filtration and kidney functions. Moreover, S+MI group, but not S alone, showed a significant increase in the expression of connective tissue growth factor (CTGF) and fibrotic proteins fibronectin (FN) and α-smooth muscle actin (SMA), in comparison to controls, in addition to a significant increase in mRNA levels of IL-6 and TNF-α inflammatory markers. Finally, reactive oxygen species (ROS) production was significantly accentuated in S+MI group concomitant with a significant increase in NOX-4 protein levels. In conclusion, smoking aggravates murine acute renal damage caused by MI at the structural and molecular levels by exacerbating renal dysfunction. |
Gribling-Burrer, A S; Leichter, M; Wurth, L; Huttin, A; Schlotter, F; Troffer-Charlier, N; Cura, V; Barkats, M; Cavarelli, J; Massenet, S; Allmang, C SECIS-binding protein 2 interacts with the SMN complex and the methylosome for selenoprotein mRNP assembly and translation. Article de journal Nucleic Acids Res, 45 (9), p. 5399-5413, 2017, ISBN: 28115638. Résumé | Liens | BibTeX | Étiquettes: ERIANI, Unité ARN @article{, title = {SECIS-binding protein 2 interacts with the SMN complex and the methylosome for selenoprotein mRNP assembly and translation.}, author = {A S Gribling-Burrer and M Leichter and L Wurth and A Huttin and F Schlotter and N Troffer-Charlier and V Cura and M Barkats and J Cavarelli and S Massenet and C Allmang}, url = {https://www.ncbi.nlm.nih.gov/pubmed/28115638?dopt=Abstract}, doi = {10.1093/nar/gkx031}, isbn = {28115638}, year = {2017}, date = {2017-01-01}, journal = {Nucleic Acids Res}, volume = {45}, number = {9}, pages = {5399-5413}, abstract = {Selenoprotein synthesis requires the co-translational recoding of a UGASec codon. This process involves an RNA structural element, called Selenocysteine Insertion Sequence (SECIS) and the SECIS binding protein 2 (SBP2). Several selenoprotein mRNAs undergo unusual cap hypermethylation by the trimethylguanosine synthase 1 (Tgs1), which is recruited by the ubiquitous Survival of MotoNeurons (SMN) protein. SMN, the protein involved in spinal muscular atrophy, is part of a chaperone complex that collaborates with the methylosome for RNP assembly. Here, we analyze the role of individual SMN and methylosome components in selenoprotein mRNP assembly and translation. We show that SBP2 interacts directly with four proteins of the SMN complex and the methylosome core proteins. Nevertheless, SBP2 is not a methylation substrate of the methylosome. We found that both SMN and methylosome complexes are required for efficient translation of the selenoprotein GPx1 in vivo We establish that the steady-state level of several selenoprotein mRNAs, major regulators of oxidative stress damage in neurons, is specifically reduced in the spinal cord of SMN-deficient mice and that cap hypermethylation of GPx1 mRNA is affected. Altogether we identified a new function of the SMN complex and the methylosome in selenoprotein mRNP assembly and expression.}, keywords = {ERIANI, Unité ARN}, pubstate = {published}, tppubtype = {article} } Selenoprotein synthesis requires the co-translational recoding of a UGASec codon. This process involves an RNA structural element, called Selenocysteine Insertion Sequence (SECIS) and the SECIS binding protein 2 (SBP2). Several selenoprotein mRNAs undergo unusual cap hypermethylation by the trimethylguanosine synthase 1 (Tgs1), which is recruited by the ubiquitous Survival of MotoNeurons (SMN) protein. SMN, the protein involved in spinal muscular atrophy, is part of a chaperone complex that collaborates with the methylosome for RNP assembly. Here, we analyze the role of individual SMN and methylosome components in selenoprotein mRNP assembly and translation. We show that SBP2 interacts directly with four proteins of the SMN complex and the methylosome core proteins. Nevertheless, SBP2 is not a methylation substrate of the methylosome. We found that both SMN and methylosome complexes are required for efficient translation of the selenoprotein GPx1 in vivo We establish that the steady-state level of several selenoprotein mRNAs, major regulators of oxidative stress damage in neurons, is specifically reduced in the spinal cord of SMN-deficient mice and that cap hypermethylation of GPx1 mRNA is affected. Altogether we identified a new function of the SMN complex and the methylosome in selenoprotein mRNP assembly and expression. |
Gross, L; Vicens, Q; Einhorn, E; Noireterre, A; Schaeffer, L; Kuhn, L; Imler, J L; Eriani, G; Meignin, C; Martin, F The IRES5'UTR of the dicistrovirus cricket paralysis virus is a type III IRES containing an essential pseudoknot structure Article de journal Nucleic Acids Res, 45 (15), p. 8993-9004, 2017, ISBN: 28911115. Résumé | Liens | BibTeX | Étiquettes: ERIANI, ERIANI HASHEM, Unité ARN @article{, title = {The IRES5'UTR of the dicistrovirus cricket paralysis virus is a type III IRES containing an essential pseudoknot structure}, author = {L Gross and Q Vicens and E Einhorn and A Noireterre and L Schaeffer and L Kuhn and J L Imler and G Eriani and C Meignin and F Martin}, url = {https://www.ncbi.nlm.nih.gov/pubmed/28911115?dopt=Abstract}, doi = {10.1093/nar/gkx622}, isbn = {28911115}, year = {2017}, date = {2017-01-01}, journal = {Nucleic Acids Res}, volume = {45}, number = {15}, pages = {8993-9004}, abstract = {Cricket paralysis virus (CrPV) is a dicistrovirus. Its positive-sense single-stranded RNA genome contains two internal ribosomal entry sites (IRESs). The 5' untranslated region (5'UTR) IRES5'UTR mediates translation of non-structural proteins encoded by ORF1 whereas the well-known intergenic region (IGR) IRESIGR is required for translation of structural proteins from open reading frame 2 in the late phase of infection. Concerted action of both IRES is essential for host translation shut-off and viral translation. IRESIGR has been extensively studied, in contrast the IRES5'UTR remains largely unexplored. Here, we define the minimal IRES element required for efficient translation initiation in drosophila S2 cell-free extracts. We show that IRES5'UTR promotes direct recruitment of the ribosome on the cognate viral AUG start codon without any scanning step, using a Hepatitis-C virus-related translation initiation mechanism. Mass spectrometry analysis revealed that IRES5'UTR recruits eukaryotic initiation factor 3, confirming that it belongs to type III class of IRES elements. Using Selective 2'-hydroxyl acylation analyzed by primer extension and DMS probing, we established a secondary structure model of 5'UTR and of the minimal IRES5'UTR. The IRES5'UTR contains a pseudoknot structure that is essential for proper folding and ribosome recruitment. Overall, our results pave the way for studies addressing the synergy and interplay between the two IRES from CrPV.}, keywords = {ERIANI, ERIANI HASHEM, Unité ARN}, pubstate = {published}, tppubtype = {article} } Cricket paralysis virus (CrPV) is a dicistrovirus. Its positive-sense single-stranded RNA genome contains two internal ribosomal entry sites (IRESs). The 5' untranslated region (5'UTR) IRES5'UTR mediates translation of non-structural proteins encoded by ORF1 whereas the well-known intergenic region (IGR) IRESIGR is required for translation of structural proteins from open reading frame 2 in the late phase of infection. Concerted action of both IRES is essential for host translation shut-off and viral translation. IRESIGR has been extensively studied, in contrast the IRES5'UTR remains largely unexplored. Here, we define the minimal IRES element required for efficient translation initiation in drosophila S2 cell-free extracts. We show that IRES5'UTR promotes direct recruitment of the ribosome on the cognate viral AUG start codon without any scanning step, using a Hepatitis-C virus-related translation initiation mechanism. Mass spectrometry analysis revealed that IRES5'UTR recruits eukaryotic initiation factor 3, confirming that it belongs to type III class of IRES elements. Using Selective 2'-hydroxyl acylation analyzed by primer extension and DMS probing, we established a secondary structure model of 5'UTR and of the minimal IRES5'UTR. The IRES5'UTR contains a pseudoknot structure that is essential for proper folding and ribosome recruitment. Overall, our results pave the way for studies addressing the synergy and interplay between the two IRES from CrPV. |
2016 |
Kowalska, J; Martin, F; Jemielity, J Synthetic Capped mRNAs for Cap-Specific Photo-Cross-Linking Experiments. incollection Rhoads, R (Ed.): Synthetic mRNA: Production, Introduction Into Cells, and Physiological Consequences, 1428 , p. 31-43, Springer Protocols, Humana Press, 2016. Résumé | BibTeX | Étiquettes: 5′, 6-thioguanosine, analogs, Binding, Cap, ERIANI, Histone, mRNA, Photo-cross-linking, stability, Transcription @incollection{, title = {Synthetic Capped mRNAs for Cap-Specific Photo-Cross-Linking Experiments.}, author = { J. Kowalska and F. Martin and J. Jemielity}, editor = { R. Rhoads}, year = {2016}, date = {2016-01-01}, booktitle = {Synthetic mRNA: Production, Introduction Into Cells, and Physiological Consequences}, volume = {1428}, pages = {31-43}, publisher = {Springer Protocols, Humana Press}, series = {Methods in Molecular Biology}, abstract = {he 7-methylguanosine triphosphate cap present at the 5' ends of eukaryotic mRNAs plays numerous roles in mRNA expression and metabolism. The identification and studies on cap-binding partners can be significantly advanced using tailored chemical tools such as synthetic cap analogues or RNAs carrying modified cap structures. Here we provide protocols for the production of mRNAs specifically labeled within the 5' cap with a nucleoside capable of being photo-activated, either 6-thioguanosine or 7-methyl-6-thioguanosine, which can be used in photo-cross-linking experiments to identify or characterize cap-binding biomolecules. We also describe a protocol for the cross-linking experiments with capped RNAs to map histone H4 cap-binding pocket.}, keywords = {5′, 6-thioguanosine, analogs, Binding, Cap, ERIANI, Histone, mRNA, Photo-cross-linking, stability, Transcription}, pubstate = {published}, tppubtype = {incollection} } he 7-methylguanosine triphosphate cap present at the 5' ends of eukaryotic mRNAs plays numerous roles in mRNA expression and metabolism. The identification and studies on cap-binding partners can be significantly advanced using tailored chemical tools such as synthetic cap analogues or RNAs carrying modified cap structures. Here we provide protocols for the production of mRNAs specifically labeled within the 5' cap with a nucleoside capable of being photo-activated, either 6-thioguanosine or 7-methyl-6-thioguanosine, which can be used in photo-cross-linking experiments to identify or characterize cap-binding biomolecules. We also describe a protocol for the cross-linking experiments with capped RNAs to map histone H4 cap-binding pocket. |
Riley, L G; Rudinger-Thirion, J; Schmitz-Abe, K; Thorburn, D R; Davis, R L; Teo, J; Arbuckle, S; Cooper, S T; Campagna, D R; Frugier, M; Markianos, K; Sue, C M; Fleming, M D; Christodoulou, J LARS2 Variants Associated with Hydrops, Lactic Acidosis, Sideroblastic Anemia, and Multisystem Failure. Book Chapter Morava, E (Ed.): JIMD Rep, 28 , p. 49-57, Springer, SSIEM, 2016, ISBN: 26537577. Résumé | Liens | BibTeX | Étiquettes: ERIANI, FRUGIER, Unité ARN @inbook{, title = {LARS2 Variants Associated with Hydrops, Lactic Acidosis, Sideroblastic Anemia, and Multisystem Failure.}, author = {L G Riley and J Rudinger-Thirion and K Schmitz-Abe and D R Thorburn and R L Davis and J Teo and S Arbuckle and S T Cooper and D R Campagna and M Frugier and K Markianos and C M Sue and M D Fleming and J Christodoulou}, editor = {E Morava}, url = {http://www.ncbi.nlm.nih.gov/pubmed/26537577?dopt=Abstract}, doi = {10.1007/8904_2015_515}, isbn = {26537577}, year = {2016}, date = {2016-01-01}, booktitle = {JIMD Rep}, volume = {28}, pages = {49-57}, publisher = {Springer}, edition = {SSIEM}, abstract = {Pathogenic variants in mitochondrial aminoacyl-tRNA synthetases result in a broad range of mitochondrial respiratory chain disorders despite their shared role in mitochondrial protein synthesis. LARS2 encodes the mitochondrial leucyl-tRNA synthetase, which attaches leucine to its cognate tRNA. Sequence variants in LARS2 have previously been associated with Perrault syndrome, characterized by premature ovarian failure and hearing loss (OMIM #615300). In this study, we report variants in LARS2 that are associated with a severe multisystem metabolic disorder. The proband was born prematurely with severe lactic acidosis, hydrops, and sideroblastic anemia. She had multisystem complications with hyaline membrane disease, impaired cardiac function, a coagulopathy, pulmonary hypertension, and progressive renal disease and succumbed at 5 days of age. Whole exome sequencing of patient DNA revealed compound heterozygous variants in LARS2 (c.1289C>T; p.Ala430Val and c.1565C>A; p.Thr522Asn). The c.1565C>A (p.Thr522Asn) LARS2 variant has previously been associated with Perrault syndrome and both identified variants are predicted to be damaging (SIFT, PolyPhen). Muscle and liver samples from the proband did not display marked mitochondrial respiratory chain enzyme deficiency. Immunoblotting of patient muscle and liver showed LARS2 levels were reduced in liver and complex I protein levels were reduced in patient muscle and liver. Aminoacylation assays revealed p.Ala430Val LARS2 had an 18-fold loss of catalytic efficiency and p.Thr522Asn a 9-fold loss compared to wild-type LARS2. We suggest that the identified LARS2 variants are responsible for the severe multisystem clinical phenotype seen in this baby and that mutations in LARS2 can result in variable phenotypes.}, keywords = {ERIANI, FRUGIER, Unité ARN}, pubstate = {published}, tppubtype = {inbook} } Pathogenic variants in mitochondrial aminoacyl-tRNA synthetases result in a broad range of mitochondrial respiratory chain disorders despite their shared role in mitochondrial protein synthesis. LARS2 encodes the mitochondrial leucyl-tRNA synthetase, which attaches leucine to its cognate tRNA. Sequence variants in LARS2 have previously been associated with Perrault syndrome, characterized by premature ovarian failure and hearing loss (OMIM #615300). In this study, we report variants in LARS2 that are associated with a severe multisystem metabolic disorder. The proband was born prematurely with severe lactic acidosis, hydrops, and sideroblastic anemia. She had multisystem complications with hyaline membrane disease, impaired cardiac function, a coagulopathy, pulmonary hypertension, and progressive renal disease and succumbed at 5 days of age. Whole exome sequencing of patient DNA revealed compound heterozygous variants in LARS2 (c.1289C>T; p.Ala430Val and c.1565C>A; p.Thr522Asn). The c.1565C>A (p.Thr522Asn) LARS2 variant has previously been associated with Perrault syndrome and both identified variants are predicted to be damaging (SIFT, PolyPhen). Muscle and liver samples from the proband did not display marked mitochondrial respiratory chain enzyme deficiency. Immunoblotting of patient muscle and liver showed LARS2 levels were reduced in liver and complex I protein levels were reduced in patient muscle and liver. Aminoacylation assays revealed p.Ala430Val LARS2 had an 18-fold loss of catalytic efficiency and p.Thr522Asn a 9-fold loss compared to wild-type LARS2. We suggest that the identified LARS2 variants are responsible for the severe multisystem clinical phenotype seen in this baby and that mutations in LARS2 can result in variable phenotypes. |
Kapps, D; Cela, M; Théobald-Dietrich, A; Hendrickson, T; Frugier, M OB or Not OB: Idiosyncratic utilization of the tRNA-binding OB-fold domain in unicellular, pathogenic eukaryotes. Article de journal FEBS Lett, 590 (23), p. 4180-4191, 2016, ISBN: 27714804. Résumé | Liens | BibTeX | Étiquettes: ERIANI, FRUGIER, FRUGIER Trbp111 parasites pathogenic eukaryotes tRNA binding protein, Unité ARN @article{, title = {OB or Not OB: Idiosyncratic utilization of the tRNA-binding OB-fold domain in unicellular, pathogenic eukaryotes.}, author = {D Kapps and M Cela and A Théobald-Dietrich and T Hendrickson and M Frugier}, url = {https://www.ncbi.nlm.nih.gov/pubmed/27714804?dopt=Abstract}, doi = {10.1002/1873-3468.12441}, isbn = {27714804}, year = {2016}, date = {2016-01-01}, journal = {FEBS Lett}, volume = {590}, number = {23}, pages = {4180-4191}, abstract = {In this Review, we examine the so-called 'OB-fold', a tRNA-binding domain homologous to the bacterial tRNA-binding protein Trbp111. We highlight the ability of OB-fold homologs to bind tRNAs and summarize their distribution in evolution. Nature has capitalized on the advantageous effects acquired when an OB-fold domain binds to tRNA by evolutionarily selecting this domain for fusion to different enzymes. Here, we review our current understanding of how the complexity of OB-fold containing proteins and enzymes developed to expand their functions, especially in unicellular, pathogenic eukaryotes. This article is protected by copyright. All rights reserved.}, keywords = {ERIANI, FRUGIER, FRUGIER Trbp111 parasites pathogenic eukaryotes tRNA binding protein, Unité ARN}, pubstate = {published}, tppubtype = {article} } In this Review, we examine the so-called 'OB-fold', a tRNA-binding domain homologous to the bacterial tRNA-binding protein Trbp111. We highlight the ability of OB-fold homologs to bind tRNAs and summarize their distribution in evolution. Nature has capitalized on the advantageous effects acquired when an OB-fold domain binds to tRNA by evolutionarily selecting this domain for fusion to different enzymes. Here, we review our current understanding of how the complexity of OB-fold containing proteins and enzymes developed to expand their functions, especially in unicellular, pathogenic eukaryotes. This article is protected by copyright. All rights reserved. |
Bour, T; Mahmoudi, N; Kapps, D; Thiberge, S; Bargieri, D; Ménard, R; Frugier, M Apicomplexa-specific tRip facilitates import of exogenous tRNAs into malaria parasites Article de journal Proc Natl Acad Sci U S A, 113 (17), p. 4717-4722, 2016, ISBN: 27071116. Résumé | Liens | BibTeX | Étiquettes: ERIANI, FRUGIER, FRUGIER Plasmodium tRNA trafficking, Unité ARN @article{, title = {Apicomplexa-specific tRip facilitates import of exogenous tRNAs into malaria parasites}, author = {T Bour and N Mahmoudi and D Kapps and S Thiberge and D Bargieri and R Ménard and M Frugier}, url = {http://www.ncbi.nlm.nih.gov/pubmed/27071116}, doi = {10.1073/pnas.1600476113}, isbn = {27071116}, year = {2016}, date = {2016-01-01}, journal = {Proc Natl Acad Sci U S A}, volume = {113}, number = {17}, pages = {4717-4722}, abstract = {The malaria-causingPlasmodiumparasites are transmitted to vertebrates by mosquitoes. To support their growth and replication, these intracellular parasites, which belong to the phylumApicomplexa,have developed mechanisms to exploit their hosts. These mechanisms include expropriation of small metabolites from infected host cells, such as purine nucleotides and amino acids. Heretofore, no evidence suggested that transfer RNAs (tRNAs) could also be exploited. We identified an unusual gene inApicomplexawith a coding sequence for membrane-docking and structure-specific tRNA binding. ThisApicomplexaprotein-designated tRip (tRNA import protein)-is anchored to the parasite plasma membrane and directs import of exogenous tRNAs. In the absence of tRip, the fitness of the parasite stage that multiplies in the blood is significantly reduced, indicating that the parasite may need host tRNAs to sustain its own translation and/or as regulatory RNAs.Plasmodiumis thus the first example, to our knowledge, of a cell importing exogenous tRNAs, suggesting a remarkable adaptation of this parasite to extend its reach into host cell biology.}, keywords = {ERIANI, FRUGIER, FRUGIER Plasmodium tRNA trafficking, Unité ARN}, pubstate = {published}, tppubtype = {article} } The malaria-causingPlasmodiumparasites are transmitted to vertebrates by mosquitoes. To support their growth and replication, these intracellular parasites, which belong to the phylumApicomplexa,have developed mechanisms to exploit their hosts. These mechanisms include expropriation of small metabolites from infected host cells, such as purine nucleotides and amino acids. Heretofore, no evidence suggested that transfer RNAs (tRNAs) could also be exploited. We identified an unusual gene inApicomplexawith a coding sequence for membrane-docking and structure-specific tRNA binding. ThisApicomplexaprotein-designated tRip (tRNA import protein)-is anchored to the parasite plasma membrane and directs import of exogenous tRNAs. In the absence of tRip, the fitness of the parasite stage that multiplies in the blood is significantly reduced, indicating that the parasite may need host tRNAs to sustain its own translation and/or as regulatory RNAs.Plasmodiumis thus the first example, to our knowledge, of a cell importing exogenous tRNAs, suggesting a remarkable adaptation of this parasite to extend its reach into host cell biology. |
Wang, Y; Zhou, X L; Ruan, Z R; Liu, R J; Eriani, G; Wang, E D A Human Disease-causing Point Mutation in Mitochondrial Threonyl-tRNA Synthetase Induces Both Structural and Functional Defects. Article de journal J Biol Chem, 291 (12), p. 6507-6520, 2016, ISBN: 26811336. Résumé | Liens | BibTeX | Étiquettes: ERIANI, ERIANI alternative splicing aminoacyl-tRNA synthetase enzyme kinetics mitochondria mitochondrial disease threonyl-tRNA synthetase, Unité ARN @article{, title = {A Human Disease-causing Point Mutation in Mitochondrial Threonyl-tRNA Synthetase Induces Both Structural and Functional Defects.}, author = {Y Wang and X L Zhou and Z R Ruan and R J Liu and G Eriani and E D Wang}, url = {http://www.ncbi.nlm.nih.gov/pubmed/26811336?dopt=Abstract}, doi = {10.1074/jbc.M115.700849}, isbn = {26811336}, year = {2016}, date = {2016-01-01}, journal = {J Biol Chem}, volume = {291}, number = {12}, pages = {6507-6520}, abstract = {Mitochondria require all translational components, including aminoacyl-tRNA synthetases (aaRSs), to complete organelle protein synthesis. Some aaRS mutations cause mitochondrial disorders, including human mitochondrial threonyl-tRNA synthetase (hmtThrRS) (encoded by TARS2), the P282L mutation of which causes mitochondrial encephalomyopathies. However, its catalytic and structural consequences remain unclear. Herein, we cloned TARS2 and purified the wild-type and P282L mutant hmtThrRS. hmtThrRS misactivates non-cognate Ser and uses post-transfer editing to clear erroneously synthesized products. In vitro and in vivo analyses revealed that the mutation induces a decrease in Thr activation, aminoacylation, and proofreading activities and a change in the protein structure and/or stability, which might cause reduced catalytic efficiency. We also identified a splicing variant of TARS2 mRNA lacking exons 8 and 9, the protein product of which is targeted into mitochondria. In HEK293T cells, the variant does not dimerize and cannot complement the ThrRS knock-out strain in yeast, suggesting that the truncated protein is inactive and might have a non-canonical function, as observed for other aaRS fragments. The present study describes the aminoacylation and editing properties of hmtThrRS, clarifies the molecular consequences of the P282L mutation, and shows that the yeast ThrRS-deletion model is suitable to test pathology-associated point mutations or alternative splicing variants of mammalian aaRS mRNAs.}, keywords = {ERIANI, ERIANI alternative splicing aminoacyl-tRNA synthetase enzyme kinetics mitochondria mitochondrial disease threonyl-tRNA synthetase, Unité ARN}, pubstate = {published}, tppubtype = {article} } Mitochondria require all translational components, including aminoacyl-tRNA synthetases (aaRSs), to complete organelle protein synthesis. Some aaRS mutations cause mitochondrial disorders, including human mitochondrial threonyl-tRNA synthetase (hmtThrRS) (encoded by TARS2), the P282L mutation of which causes mitochondrial encephalomyopathies. However, its catalytic and structural consequences remain unclear. Herein, we cloned TARS2 and purified the wild-type and P282L mutant hmtThrRS. hmtThrRS misactivates non-cognate Ser and uses post-transfer editing to clear erroneously synthesized products. In vitro and in vivo analyses revealed that the mutation induces a decrease in Thr activation, aminoacylation, and proofreading activities and a change in the protein structure and/or stability, which might cause reduced catalytic efficiency. We also identified a splicing variant of TARS2 mRNA lacking exons 8 and 9, the protein product of which is targeted into mitochondria. In HEK293T cells, the variant does not dimerize and cannot complement the ThrRS knock-out strain in yeast, suggesting that the truncated protein is inactive and might have a non-canonical function, as observed for other aaRS fragments. The present study describes the aminoacylation and editing properties of hmtThrRS, clarifies the molecular consequences of the P282L mutation, and shows that the yeast ThrRS-deletion model is suitable to test pathology-associated point mutations or alternative splicing variants of mammalian aaRS mRNAs. |
Wang, M; Liu, H; Zheng, J; Chen, B; Zhou, M; Fan, W; Wang, H; Liang, X; Zhou, X; Eriani, G; Jiang, P; Guan, M X A deafness and diabetes associated tRNA mutation caused the deficient pseudouridinylation at position 55 in tRNAGlu and mitochondrial dysfunction. Article de journal J Biol Chem, 291 (40), p. 21029-21041, 2016, ISBN: 27519417. Résumé | Liens | BibTeX | Étiquettes: ERIANI, ERIANI diabetes hearing mitochondrial DNA (mtDNA) mitochondrial disease mutant pathogenesis post-translational modification (PTM) transfer RNA (tRNA), Unité ARN @article{, title = {A deafness and diabetes associated tRNA mutation caused the deficient pseudouridinylation at position 55 in tRNAGlu and mitochondrial dysfunction.}, author = {M Wang and H Liu and J Zheng and B Chen and M Zhou and W Fan and H Wang and X Liang and X Zhou and G Eriani and P Jiang and M X Guan}, url = {http://www.ncbi.nlm.nih.gov/pubmed/27519417?dopt=Abstract}, doi = {10.1074/jbc.M116.739482}, isbn = {27519417}, year = {2016}, date = {2016-01-01}, journal = {J Biol Chem}, volume = {291}, number = {40}, pages = {21029-21041}, abstract = {Several mitochondrial tRNA mutations have been associated with maternally inherited diabetes and deafness (MIDD). However, the pathophysiology of these tRNA mutations remains poorly understood. In this report, we identified the novel homoplasmic 14692A>G mutation in the mitochondrial tRNAGlu gene among three Han Chinese families with maternally inherited diabetes and deafness. The m.14692A>G mutation affected a highly conserved uridine at position 55 of TΨC loop of tRNAGlu. The uridine is modified to pseudouridine (Ψ55), which plays an important role in the structure and function of this tRNA. Using lymphoblastoid cell lines derived from a Chinese family, we demonstrated that the m.14692A>G mutation caused the loss of Ψ55 modification and increased the angiogenin-mediated endonucleolytic cleavage in mutant tRNAGlu. The destabilization of base-pairing (18A-Ψ55) caused by the m.14692A>G mutation perturbed the conformation and stability of tRNAGlu. Approximately 65% decrease in the steady-state level of tRNAGlu was observed in mutant cells, compared to control cells. A failure in tRNAGlu metabolism impaired mitochondrial translation, especially for polypeptides with high proportion of glutamic acid codons such as MT-ND1, MT-ND6 and MT-CO2 in mutant cells. An impairment of mitochondrial translation caused the defective respiratory capacity, especially reducing activities of complexes I and IV. Furthermore, marked decreases in the levels of mitochondrial ATP and membrane potential were observed in mutant cells. These mitochondrial dysfunctions caused an increasing production of reactive oxygen species in the mutant cells. Our findings may provide new insights into pathophysiology of MIDD, which was primarily manifested by the deficient nucleotide modification of mitochondrial tRNAGlu.}, keywords = {ERIANI, ERIANI diabetes hearing mitochondrial DNA (mtDNA) mitochondrial disease mutant pathogenesis post-translational modification (PTM) transfer RNA (tRNA), Unité ARN}, pubstate = {published}, tppubtype = {article} } Several mitochondrial tRNA mutations have been associated with maternally inherited diabetes and deafness (MIDD). However, the pathophysiology of these tRNA mutations remains poorly understood. In this report, we identified the novel homoplasmic 14692A>G mutation in the mitochondrial tRNAGlu gene among three Han Chinese families with maternally inherited diabetes and deafness. The m.14692A>G mutation affected a highly conserved uridine at position 55 of TΨC loop of tRNAGlu. The uridine is modified to pseudouridine (Ψ55), which plays an important role in the structure and function of this tRNA. Using lymphoblastoid cell lines derived from a Chinese family, we demonstrated that the m.14692A>G mutation caused the loss of Ψ55 modification and increased the angiogenin-mediated endonucleolytic cleavage in mutant tRNAGlu. The destabilization of base-pairing (18A-Ψ55) caused by the m.14692A>G mutation perturbed the conformation and stability of tRNAGlu. Approximately 65% decrease in the steady-state level of tRNAGlu was observed in mutant cells, compared to control cells. A failure in tRNAGlu metabolism impaired mitochondrial translation, especially for polypeptides with high proportion of glutamic acid codons such as MT-ND1, MT-ND6 and MT-CO2 in mutant cells. An impairment of mitochondrial translation caused the defective respiratory capacity, especially reducing activities of complexes I and IV. Furthermore, marked decreases in the levels of mitochondrial ATP and membrane potential were observed in mutant cells. These mitochondrial dysfunctions caused an increasing production of reactive oxygen species in the mutant cells. Our findings may provide new insights into pathophysiology of MIDD, which was primarily manifested by the deficient nucleotide modification of mitochondrial tRNAGlu. |
McShane, A; Hok, E; Tomberlin, J; Eriani, G; Geslain, R The Enzymatic Paradox of Yeast Arginyl-tRNA Synthetase: Exclusive Arginine Transfer Controlled by a Flexible Mechanism of tRNA Recognition. Article de journal PLoS One, 11 (2), p. e0148460, 2016, ISBN: 26844776. Résumé | Liens | BibTeX | Étiquettes: ERIANI, Unité ARN @article{, title = {The Enzymatic Paradox of Yeast Arginyl-tRNA Synthetase: Exclusive Arginine Transfer Controlled by a Flexible Mechanism of tRNA Recognition.}, author = {A McShane and E Hok and J Tomberlin and G Eriani and R Geslain}, url = {http://www.ncbi.nlm.nih.gov/pubmed/26844776?dopt=Abstract}, doi = {10.1371/journal.pone.0148460}, isbn = {26844776}, year = {2016}, date = {2016-01-01}, journal = {PLoS One}, volume = {11}, number = {2}, pages = {e0148460}, abstract = {Identity determinants are essential for the accurate recognition of transfer RNAs by aminoacyl-tRNA synthetases. To date, arginine determinants in the yeast Saccharomyces cerevisiae have been identified exclusively in vitro and only on a limited number of tRNA Arginine isoacceptors. In the current study, we favor a full cellular approach and expand the investigation of arginine determinants to all four tRNA Arg isoacceptors. More precisely, this work scrutinizes the relevance of the tRNA nucleotides at position 20, 35 and 36 in the yeast arginylation reaction. We built 21 mutants by site-directed mutagenesis and tested their functionality in YAL5, a previously engineered yeast knockout deficient for the expression of tRNA Arg CCG. Arginylation levels were also monitored using Northern blot. Our data collected in vivo correlate with previous observations. C35 is the prominent arginine determinant followed by G36 or U36 (G/U36). In addition, although there is no major arginine determinant in the D loop, the recognition of tRNA Arg ICG relies to some extent on the nucleotide at position 20. This work refines the existing model for tRNA Arg recognition. Our observations indicate that yeast Arginyl-tRNA synthetase (yArgRS) relies on distinct mechanisms to aminoacylate the four isoacceptors. Finally, according to our refined model, yArgRS is able to accommodate tRNA Arg scaffolds presenting N34, C/G35 and G/A/U36 anticodons while maintaining specificity. We discuss the mechanistic and potential physiological implications of these findings.}, keywords = {ERIANI, Unité ARN}, pubstate = {published}, tppubtype = {article} } Identity determinants are essential for the accurate recognition of transfer RNAs by aminoacyl-tRNA synthetases. To date, arginine determinants in the yeast Saccharomyces cerevisiae have been identified exclusively in vitro and only on a limited number of tRNA Arginine isoacceptors. In the current study, we favor a full cellular approach and expand the investigation of arginine determinants to all four tRNA Arg isoacceptors. More precisely, this work scrutinizes the relevance of the tRNA nucleotides at position 20, 35 and 36 in the yeast arginylation reaction. We built 21 mutants by site-directed mutagenesis and tested their functionality in YAL5, a previously engineered yeast knockout deficient for the expression of tRNA Arg CCG. Arginylation levels were also monitored using Northern blot. Our data collected in vivo correlate with previous observations. C35 is the prominent arginine determinant followed by G36 or U36 (G/U36). In addition, although there is no major arginine determinant in the D loop, the recognition of tRNA Arg ICG relies to some extent on the nucleotide at position 20. This work refines the existing model for tRNA Arg recognition. Our observations indicate that yeast Arginyl-tRNA synthetase (yArgRS) relies on distinct mechanisms to aminoacylate the four isoacceptors. Finally, according to our refined model, yArgRS is able to accommodate tRNA Arg scaffolds presenting N34, C/G35 and G/A/U36 anticodons while maintaining specificity. We discuss the mechanistic and potential physiological implications of these findings. |
Martin, F; Ménétret, J F; Simonetti, A; Myasnikov, A G; Vicens, Q; Prongidi-Fix, L; Natchiar, S K; Klaholz, B P; Eriani, G Ribosomal 18S rRNA base pairs with mRNA during eukaryotic translation initiation. Article de journal Nat Commun, 7 , p. 12622, 2016, ISBN: 27554013. Résumé | Liens | BibTeX | Étiquettes: ERIANI, Unité ARN @article{, title = {Ribosomal 18S rRNA base pairs with mRNA during eukaryotic translation initiation.}, author = {F Martin and J F Ménétret and A Simonetti and A G Myasnikov and Q Vicens and L Prongidi-Fix and S K Natchiar and B P Klaholz and G Eriani}, url = {http://www.ncbi.nlm.nih.gov/pubmed/27554013?dopt=Abstract}, doi = {10.1038/ncomms12622}, isbn = {27554013}, year = {2016}, date = {2016-01-01}, journal = {Nat Commun}, volume = {7}, pages = {12622}, abstract = {Eukaryotic mRNAs often contain a Kozak sequence that helps tether the ribosome to the AUG start codon. The mRNA of histone H4 (h4) does not undergo classical ribosome scanning but has evolved a specific tethering mechanism. The cryo-EM structure of the rabbit ribosome complex with mouse h4 shows that the mRNA forms a folded, repressive structure at the mRNA entry site on the 40S subunit next to the tip of helix 16 of 18S ribosomal RNA (rRNA). Toe-printing and mutational assays reveal that an interaction exists between a purine-rich sequence in h4 mRNA and a complementary UUUC sequence of helix h16. Together the present data establish that the h4 mRNA harbours a sequence complementary to an 18S rRNA sequence which tethers the mRNA to the ribosome to promote proper start codon positioning, complementing the interactions of the 40S subunit with the Kozak sequence that flanks the AUG start codon.}, keywords = {ERIANI, Unité ARN}, pubstate = {published}, tppubtype = {article} } Eukaryotic mRNAs often contain a Kozak sequence that helps tether the ribosome to the AUG start codon. The mRNA of histone H4 (h4) does not undergo classical ribosome scanning but has evolved a specific tethering mechanism. The cryo-EM structure of the rabbit ribosome complex with mouse h4 shows that the mRNA forms a folded, repressive structure at the mRNA entry site on the 40S subunit next to the tip of helix 16 of 18S ribosomal RNA (rRNA). Toe-printing and mutational assays reveal that an interaction exists between a purine-rich sequence in h4 mRNA and a complementary UUUC sequence of helix h16. Together the present data establish that the h4 mRNA harbours a sequence complementary to an 18S rRNA sequence which tethers the mRNA to the ribosome to promote proper start codon positioning, complementing the interactions of the 40S subunit with the Kozak sequence that flanks the AUG start codon. |
2015 |
Alexandrova, J; Paulus, C; Rudinger-Thirion, J; Jossinet, F; Frugier, M Elaborate uORF/IRES features control expression and localization of human glycyl-tRNA synthetase. Article de journal RNA Biol, 12 (12), p. 1301-1313, 2015, ISBN: 26327585. Résumé | Liens | BibTeX | Étiquettes: ERIANI, FRUGIER, FRUGIER JOSSINET Aminoacyl-tRNA synthetase IRES post-transcriptional control uORF, Unité ARN @article{, title = {Elaborate uORF/IRES features control expression and localization of human glycyl-tRNA synthetase.}, author = {J Alexandrova and C Paulus and J Rudinger-Thirion and F Jossinet and M Frugier}, url = {http://www.ncbi.nlm.nih.gov/pubmed/26327585?dopt=Abstract}, doi = {10.1080/15476286.2015.1086866}, isbn = {26327585}, year = {2015}, date = {2015-01-01}, journal = {RNA Biol}, volume = {12}, number = {12}, pages = {1301-1313}, abstract = {The canonical activity of glycyl-tRNA synthetase (GARS) is to charge glycine onto its cognate tRNAs. However, outside translation, GARS also participates in many other functions. A single gene encodes both the cytosolic and mitochondrial forms of GARS but two mRNA isoforms were identified. Using immunolocalization assays, in vitro translation assays and bicistronic constructs we provide experimental evidence that one of these mRNAs tightly controls expression and localization of human GARS. An intricate regulatory domain was found in its 5'-UTR which displays a functional Internal Ribosome Entry Site and an upstream Open Reading Frame. Together, these elements hinder the synthesis of the mitochondrial GARS and target the translation of the cytosolic enzyme to ER-bound ribosomes. This finding reveals a complex picture of GARS translation and localization in mammals. In this context, we discuss how human GARS expression could influence its moonlighting activities and its involvement in diseases.}, keywords = {ERIANI, FRUGIER, FRUGIER JOSSINET Aminoacyl-tRNA synthetase IRES post-transcriptional control uORF, Unité ARN}, pubstate = {published}, tppubtype = {article} } The canonical activity of glycyl-tRNA synthetase (GARS) is to charge glycine onto its cognate tRNAs. However, outside translation, GARS also participates in many other functions. A single gene encodes both the cytosolic and mitochondrial forms of GARS but two mRNA isoforms were identified. Using immunolocalization assays, in vitro translation assays and bicistronic constructs we provide experimental evidence that one of these mRNAs tightly controls expression and localization of human GARS. An intricate regulatory domain was found in its 5'-UTR which displays a functional Internal Ribosome Entry Site and an upstream Open Reading Frame. Together, these elements hinder the synthesis of the mitochondrial GARS and target the translation of the cytosolic enzyme to ER-bound ribosomes. This finding reveals a complex picture of GARS translation and localization in mammals. In this context, we discuss how human GARS expression could influence its moonlighting activities and its involvement in diseases. |
Yan, W; Ye, Q; Tan, M; Chen, X; Eriani, G; Wang, E D Modulation of aminoacylation and editing properties of leucyl-tRNA synthetase by a conserved structural module. Article de journal J Biol Chem, 290 (19), p. 12256-12267, 2015, ISBN: 25817995. Résumé | Liens | BibTeX | Étiquettes: ERIANI, ERIANI aminoacyl tRNA synthetase aminoacylation editing enzyme evolution protein synthesis stem contact fold transfer RNA (tRNA), Unité ARN @article{, title = {Modulation of aminoacylation and editing properties of leucyl-tRNA synthetase by a conserved structural module.}, author = {W Yan and Q Ye and M Tan and X Chen and G Eriani and E D Wang}, url = {http://www.ncbi.nlm.nih.gov/pubmed/25817995?dopt=Abstract}, doi = {10.1074/jbc.M115.639492}, isbn = {25817995}, year = {2015}, date = {2015-01-01}, journal = {J Biol Chem}, volume = {290}, number = {19}, pages = {12256-12267}, abstract = {A conserved structural module following the KMSKS catalytic loop exhibits α-α-β-α topology in class Ia and Ib aminoacyl-tRNA synthetases. However, the function of this domain has received little attention. Here, we describe the effect this module has on the aminoacylation and editing capacities of leucyl-tRNA synthetases (LeuRSs) by characterizing the key residues from various species. Mutation of highly conserved basic residues on the third α-helix of this domain impairs the affinity of LeuRS for the anticodon stem of tRNALeu, which decreases both aminoacylation and editing activities. Two glycine residues on this α-helix contribute to flexibility, leucine activation and editing of LeuRS from Escherichia coli (EcLeuRS). Acidic residues on the β-strand enhance the editing activity of EcLeuRS and sense the size of the tRNALeu D-loop. Incorporation of these residues stimulates the tRNA-dependent editing activity of the chimeric minimalist enzyme MmLeuRS fused with the connective polypeptide 1 (CP1) editing domain and leucine-specific domain of (LSD) from EcLeuRS. Together, these results reveal the stem contact (SC)-fold to be functional as well as a structural linker between the catalytic site and tRNA binding domain. Sequence comparison of the EcLeuRS SC-fold domain with editing-deficient enzymes suggests that key residues of this module have evolved an adaptive strategy to follow the editing functions of LeuRSs.}, keywords = {ERIANI, ERIANI aminoacyl tRNA synthetase aminoacylation editing enzyme evolution protein synthesis stem contact fold transfer RNA (tRNA), Unité ARN}, pubstate = {published}, tppubtype = {article} } A conserved structural module following the KMSKS catalytic loop exhibits α-α-β-α topology in class Ia and Ib aminoacyl-tRNA synthetases. However, the function of this domain has received little attention. Here, we describe the effect this module has on the aminoacylation and editing capacities of leucyl-tRNA synthetases (LeuRSs) by characterizing the key residues from various species. Mutation of highly conserved basic residues on the third α-helix of this domain impairs the affinity of LeuRS for the anticodon stem of tRNALeu, which decreases both aminoacylation and editing activities. Two glycine residues on this α-helix contribute to flexibility, leucine activation and editing of LeuRS from Escherichia coli (EcLeuRS). Acidic residues on the β-strand enhance the editing activity of EcLeuRS and sense the size of the tRNALeu D-loop. Incorporation of these residues stimulates the tRNA-dependent editing activity of the chimeric minimalist enzyme MmLeuRS fused with the connective polypeptide 1 (CP1) editing domain and leucine-specific domain of (LSD) from EcLeuRS. Together, these results reveal the stem contact (SC)-fold to be functional as well as a structural linker between the catalytic site and tRNA binding domain. Sequence comparison of the EcLeuRS SC-fold domain with editing-deficient enzymes suggests that key residues of this module have evolved an adaptive strategy to follow the editing functions of LeuRSs. |
Ruan, Z R; Fang, Z P; Ye, Q; Lei, H Y; Eriani, G; Zhou, X L; Wang, E D Identification of Lethal Mutations in Yeast Threonyl-tRNA Synthetase Revealing Critical Residues in Its Human Homolog. Article de journal J Biol Chem, 290 (3), p. 1664-1678, 2015, ISBN: 25416776. Résumé | Liens | BibTeX | Étiquettes: ERIANI, ERIANI aminoacyl tRNA synthetase aminoacylation editing mutagenesis protein structure transfer RNA (tRNA) translation, Unité ARN @article{, title = {Identification of Lethal Mutations in Yeast Threonyl-tRNA Synthetase Revealing Critical Residues in Its Human Homolog.}, author = {Z R Ruan and Z P Fang and Q Ye and H Y Lei and G Eriani and X L Zhou and E D Wang}, url = {http://www.ncbi.nlm.nih.gov/pubmed/25416776?dopt=Abstract}, doi = {10.1074/jbc.M114.599886}, isbn = {25416776}, year = {2015}, date = {2015-01-01}, journal = {J Biol Chem}, volume = {290}, number = {3}, pages = {1664-1678}, abstract = {Aminoacyl-tRNA synthetases (aaRSs) are a group of ancient enzymes catalyzing aminoacylation and editing reactions for protein biosynthesis. Increasing evidence suggests that these critical enzymes are often associated with mammalian disorders. Therefore, complete determination of the enzymes functions is essential for informed diagnosis and treatment. Here, we show that a yeast knockout strain for the threonyl-tRNA synthetase (ThrRS) gene is an excellent platform for such an investigation. Saccharomyces cerevisiae ThrRS (ScThrRS) has a unique modular structure containing four structural domains and a eukaryotic-specific N-terminal extension. Using randomly mutated libraries of the ThrRS gene (thrS) and a genetic screen, a set of loss-of-function mutants were identified. The mutations affected the synthetic and editing activities and influenced the dimer interface. The results also highlighted the role of the N-terminal extension for enzymatic activity and protein stability. To gain insights into the pathological mechanisms induced by mutated aaRSs, we systematically introduced the loss-of-function mutations into the human cytoplasmic ThrRS gene. All mutations induced similar detrimental effects, showing that the yeast model could be used to study pathology-associated point mutations in mammalian aaRSs.}, keywords = {ERIANI, ERIANI aminoacyl tRNA synthetase aminoacylation editing mutagenesis protein structure transfer RNA (tRNA) translation, Unité ARN}, pubstate = {published}, tppubtype = {article} } Aminoacyl-tRNA synthetases (aaRSs) are a group of ancient enzymes catalyzing aminoacylation and editing reactions for protein biosynthesis. Increasing evidence suggests that these critical enzymes are often associated with mammalian disorders. Therefore, complete determination of the enzymes functions is essential for informed diagnosis and treatment. Here, we show that a yeast knockout strain for the threonyl-tRNA synthetase (ThrRS) gene is an excellent platform for such an investigation. Saccharomyces cerevisiae ThrRS (ScThrRS) has a unique modular structure containing four structural domains and a eukaryotic-specific N-terminal extension. Using randomly mutated libraries of the ThrRS gene (thrS) and a genetic screen, a set of loss-of-function mutants were identified. The mutations affected the synthetic and editing activities and influenced the dimer interface. The results also highlighted the role of the N-terminal extension for enzymatic activity and protein stability. To gain insights into the pathological mechanisms induced by mutated aaRSs, we systematically introduced the loss-of-function mutations into the human cytoplasmic ThrRS gene. All mutations induced similar detrimental effects, showing that the yeast model could be used to study pathology-associated point mutations in mammalian aaRSs. |
Lei, H Y; Zhou, X L; Ruan, Z R; Sun, W C; Eriani, G; Wang, E D Calpain Cleaves Most Components in the Multiple Aminoacyl-tRNA Synthetase Complex and Affects Their Functions. Article de journal J Biol Chem, 290 (43), p. 26314-26327, 2015, ISBN: 26324710. Résumé | Liens | BibTeX | Étiquettes: ERIANI, ERIANI aminoacyl tRNA synthetase aminoacylation calpain protein fragments protein secretion proteolysis stress, Unité ARN @article{, title = {Calpain Cleaves Most Components in the Multiple Aminoacyl-tRNA Synthetase Complex and Affects Their Functions.}, author = {H Y Lei and X L Zhou and Z R Ruan and W C Sun and G Eriani and E D Wang}, url = {http://www.ncbi.nlm.nih.gov/pubmed/26324710?dopt=Abstract}, doi = {10.1074/jbc.M115.681999}, isbn = {26324710}, year = {2015}, date = {2015-01-01}, journal = {J Biol Chem}, volume = {290}, number = {43}, pages = {26314-26327}, abstract = {Nine aminoacyl-tRNA synthetases (aaRSs) and three scaffold proteins form a super multiple aminoacyl-tRNA synthetase complex (MSC) in the human cytoplasm. Domains that have been added progressively to MSC components during evolution are linked by unstructured flexible peptides, producing an elongated and multiarmed MSC structure that is easily attacked by proteases in vivo. A yeast two-hybrid screen for proteins interacting with LeuRS, a representative MSC member, identified calpain 2, a calcium-activated neutral cysteine protease. Calpain 2 and calpain 1 could partially hydrolyze most MSC components to generate specific fragments that resembled those reported previously. The cleavage sites of calpain in ArgRS, GlnRS, and p43 were precisely mapped. After cleavage, their N-terminal regions were removed. Sixty-three amino acid residues were removed from the N terminus of ArgRS to form ArgRSΔN63; GlnRS formed GlnRSΔN198, and p43 formed p43ΔN106. GlnRSΔN198 had a much weaker affinity for its substrates, tRNA(Gln) and glutamine. p43ΔN106 was the same as the previously reported p43-derived apoptosis-released factor. The formation of p43ΔN106 by calpain depended on Ca(2+) and could be specifically inhibited by calpeptin and by RNAi of the regulatory subunit of calpain in vivo. These results showed, for the first time, that calpain plays an essential role in dissociating the MSC and might regulate the canonical and non-canonical functions of certain components of the MSC.}, keywords = {ERIANI, ERIANI aminoacyl tRNA synthetase aminoacylation calpain protein fragments protein secretion proteolysis stress, Unité ARN}, pubstate = {published}, tppubtype = {article} } Nine aminoacyl-tRNA synthetases (aaRSs) and three scaffold proteins form a super multiple aminoacyl-tRNA synthetase complex (MSC) in the human cytoplasm. Domains that have been added progressively to MSC components during evolution are linked by unstructured flexible peptides, producing an elongated and multiarmed MSC structure that is easily attacked by proteases in vivo. A yeast two-hybrid screen for proteins interacting with LeuRS, a representative MSC member, identified calpain 2, a calcium-activated neutral cysteine protease. Calpain 2 and calpain 1 could partially hydrolyze most MSC components to generate specific fragments that resembled those reported previously. The cleavage sites of calpain in ArgRS, GlnRS, and p43 were precisely mapped. After cleavage, their N-terminal regions were removed. Sixty-three amino acid residues were removed from the N terminus of ArgRS to form ArgRSΔN63; GlnRS formed GlnRSΔN198, and p43 formed p43ΔN106. GlnRSΔN198 had a much weaker affinity for its substrates, tRNA(Gln) and glutamine. p43ΔN106 was the same as the previously reported p43-derived apoptosis-released factor. The formation of p43ΔN106 by calpain depended on Ca(2+) and could be specifically inhibited by calpeptin and by RNAi of the regulatory subunit of calpain in vivo. These results showed, for the first time, that calpain plays an essential role in dissociating the MSC and might regulate the canonical and non-canonical functions of certain components of the MSC. |
Eriani, G; Karam, J; Jacinto, J; Richard, Morris E; Geslain, R MIST, a Novel Approach to Reveal Hidden Substrate Specificity in Aminoacyl-tRNA Synthetases. Article de journal PLoS One, 10 (6), p. e0130042, 2015, ISBN: 26067673. Résumé | Liens | BibTeX | Étiquettes: ERIANI, Unité ARN @article{, title = {MIST, a Novel Approach to Reveal Hidden Substrate Specificity in Aminoacyl-tRNA Synthetases.}, author = {G Eriani and J Karam and J Jacinto and E Morris Richard and R Geslain}, url = {http://www.ncbi.nlm.nih.gov/pubmed/26067673?dopt=Abstract}, doi = {10.1371/journal.pone.0130042}, isbn = {26067673}, year = {2015}, date = {2015-01-01}, journal = {PLoS One}, volume = {10}, number = {6}, pages = {e0130042}, abstract = {Aminoacyl-tRNA synthetases (AARSs) constitute a family of RNA-binding proteins, that participate in the translation of the genetic code, by covalently linking amino acids to appropriate tRNAs. Due to their fundamental importance for cell life, AARSs are likely to be one of the most ancient families of enzymes and have therefore been characterized extensively. Paradoxically, little is known about their capacity to discriminate tRNAs mainly because of the practical challenges that represent precise and systematic tRNA identification. This work describes a new technical and conceptual approach named MIST (Microarray Identification of Shifted tRNAs) designed to study the formation of tRNA/AARS complexes independently from the aminoacylation reaction. MIST combines electrophoretic mobility shift assays with microarray analyses. Although MIST is a non-cellular assay, it fully integrates the notion of tRNA competition. In this study we focus on yeast cytoplasmic Arginyl-tRNA synthetase (yArgRS) and investigate in depth its ability to discriminate cellular tRNAs. We report that yArgRS in submicromolar concentrations binds cognate and non-cognate tRNAs with a wide range of apparent affinities. In particular, we demonstrate that yArgRS binds preferentially to type II tRNAs but does not support their misaminoacylation. Our results reveal important new trends in tRNA/AARS complex formation and potential deep physiological implications.}, keywords = {ERIANI, Unité ARN}, pubstate = {published}, tppubtype = {article} } Aminoacyl-tRNA synthetases (AARSs) constitute a family of RNA-binding proteins, that participate in the translation of the genetic code, by covalently linking amino acids to appropriate tRNAs. Due to their fundamental importance for cell life, AARSs are likely to be one of the most ancient families of enzymes and have therefore been characterized extensively. Paradoxically, little is known about their capacity to discriminate tRNAs mainly because of the practical challenges that represent precise and systematic tRNA identification. This work describes a new technical and conceptual approach named MIST (Microarray Identification of Shifted tRNAs) designed to study the formation of tRNA/AARS complexes independently from the aminoacylation reaction. MIST combines electrophoretic mobility shift assays with microarray analyses. Although MIST is a non-cellular assay, it fully integrates the notion of tRNA competition. In this study we focus on yeast cytoplasmic Arginyl-tRNA synthetase (yArgRS) and investigate in depth its ability to discriminate cellular tRNAs. We report that yArgRS in submicromolar concentrations binds cognate and non-cognate tRNAs with a wide range of apparent affinities. In particular, we demonstrate that yArgRS binds preferentially to type II tRNAs but does not support their misaminoacylation. Our results reveal important new trends in tRNA/AARS complex formation and potential deep physiological implications. |
Chicher, J; Simonetti, A; Kuhn, L; Schaeffer, L; Hammann, P; Eriani, G; Martin, F Purification of mRNA-programmed translation initiation complexes suitable for mass spectrometry analysis. Article de journal Proteomics, 15 (14), p. 2417-2425, 2015, ISBN: 25914180. Résumé | Liens | BibTeX | Étiquettes: ERIANI, ERIANI RNA binding proteins Ribosome Translation initiation mRNA stability, Unité ARN @article{, title = {Purification of mRNA-programmed translation initiation complexes suitable for mass spectrometry analysis.}, author = {J Chicher and A Simonetti and L Kuhn and L Schaeffer and P Hammann and G Eriani and F Martin}, url = {http://www.ncbi.nlm.nih.gov/pubmed/25914180?dopt=Abstract}, doi = {10.1002/pmic.201400628}, isbn = {25914180}, year = {2015}, date = {2015-01-01}, journal = {Proteomics}, volume = {15}, number = {14}, pages = {2417-2425}, abstract = {Liquid Chromatography coupled to tandem Mass Spectrometry (nanoLC-MS/MS) is a powerful analytical technique for the identification and mass analysis of complex protein mixtures. Here we present a combination of methods developed for the extensive/deep proteomic analysis of purified ribosome/mRNA particles assembled in rabbit reticulocyte lysate (RRL). Ribosomes are assembled on chimeric biotinylated mRNA-DNA molecules immobilized on streptavidin-coated beads and incubated with RRL to form initiation complexes. After washing steps, the complexes are trypsin-digested directly on the beads in semi-native condition or after their elution from the beads in denaturing Laemmli buffer. The nanoLC-MS/MS analysis performed on complexes assembled on β-globin, viral HCV and histone H4 mRNAs revealed significant differences in initiation factors composition in agreement with models of translation initiation used by these different types of mRNAs. Using Laemmli-denaturing condition induces release of deeply buried peptides from the ribosome and eukaryotic initiation factor 3 (eIF3) allowing the identification of the nearly complete set of ribosomal proteins. This article is protected by copyright. All rights reserved.}, keywords = {ERIANI, ERIANI RNA binding proteins Ribosome Translation initiation mRNA stability, Unité ARN}, pubstate = {published}, tppubtype = {article} } Liquid Chromatography coupled to tandem Mass Spectrometry (nanoLC-MS/MS) is a powerful analytical technique for the identification and mass analysis of complex protein mixtures. Here we present a combination of methods developed for the extensive/deep proteomic analysis of purified ribosome/mRNA particles assembled in rabbit reticulocyte lysate (RRL). Ribosomes are assembled on chimeric biotinylated mRNA-DNA molecules immobilized on streptavidin-coated beads and incubated with RRL to form initiation complexes. After washing steps, the complexes are trypsin-digested directly on the beads in semi-native condition or after their elution from the beads in denaturing Laemmli buffer. The nanoLC-MS/MS analysis performed on complexes assembled on β-globin, viral HCV and histone H4 mRNAs revealed significant differences in initiation factors composition in agreement with models of translation initiation used by these different types of mRNAs. Using Laemmli-denaturing condition induces release of deeply buried peptides from the ribosome and eukaryotic initiation factor 3 (eIF3) allowing the identification of the nearly complete set of ribosomal proteins. This article is protected by copyright. All rights reserved. |
2014 |
Wurth, L; Gribling-Burrer, A S; Verheggen, C; Leichter, M; Takeuchi, A; Baudrey, S; Martin, F; Krol, A; Bertrand, E; Allmang, C Hypermethylated-capped selenoprotein mRNAs in mammals. Article de journal Nucleic Acids Res, 42 (13), p. 8663-8677, 2014, ISBN: 25013170. Résumé | Liens | BibTeX | Étiquettes: ERIANI, Unité ARN @article{, title = {Hypermethylated-capped selenoprotein mRNAs in mammals.}, author = {L Wurth and A S Gribling-Burrer and C Verheggen and M Leichter and A Takeuchi and S Baudrey and F Martin and A Krol and E Bertrand and C Allmang}, url = {http://www.ncbi.nlm.nih.gov/pubmed/25013170}, doi = {10.1093/nar/gku580}, isbn = {25013170}, year = {2014}, date = {2014-01-01}, journal = {Nucleic Acids Res}, volume = {42}, number = {13}, pages = {8663-8677}, abstract = {Mammalian mRNAs are generated by complex and coordinated biogenesis pathways and acquire 5'-end m7G caps that play fundamental roles in processing and translation. Here we show that several selenoprotein mRNAs are not recognized efficiently by translation initiation factor eIF4E because they bear a hypermethylated cap. This cap modification is acquired via a 5'-end maturation pathway similar to that of the small nucle(ol)ar RNAs (sn- and snoRNAs). Our findings also establish that the trimethylguanosine synthase 1 (Tgs1) interacts with selenoprotein mRNAs for cap hypermethylation and that assembly chaperones and core proteins devoted to sn- and snoRNP maturation contribute to recruiting Tgs1 to selenoprotein mRNPs. We further demonstrate that the hypermethylated-capped selenoprotein mRNAs localize to the cytoplasm, are associated with polysomes and thus translated. Moreover, we found that the activity of Tgs1, but not of eIF4E, is required for the synthesis of the GPx1 selenoprotein in vivo.}, keywords = {ERIANI, Unité ARN}, pubstate = {published}, tppubtype = {article} } Mammalian mRNAs are generated by complex and coordinated biogenesis pathways and acquire 5'-end m7G caps that play fundamental roles in processing and translation. Here we show that several selenoprotein mRNAs are not recognized efficiently by translation initiation factor eIF4E because they bear a hypermethylated cap. This cap modification is acquired via a 5'-end maturation pathway similar to that of the small nucle(ol)ar RNAs (sn- and snoRNAs). Our findings also establish that the trimethylguanosine synthase 1 (Tgs1) interacts with selenoprotein mRNAs for cap hypermethylation and that assembly chaperones and core proteins devoted to sn- and snoRNP maturation contribute to recruiting Tgs1 to selenoprotein mRNPs. We further demonstrate that the hypermethylated-capped selenoprotein mRNAs localize to the cytoplasm, are associated with polysomes and thus translated. Moreover, we found that the activity of Tgs1, but not of eIF4E, is required for the synthesis of the GPx1 selenoprotein in vivo. |
Ray, S; Blaise, M; Roy, B; Ghosh, S; Kern, D; Banerjee, R Fusion with Anticodon Binding Domain of GluRS is Not Sufficient to Alter the Substrate Specificity of a Chimeric Glu-Q-RS. Article de journal Protein J, 33 (1), p. 48-60, 2014, ISBN: 24374508. Résumé | Liens | BibTeX | Étiquettes: ERIANI, Unité ARN @article{, title = {Fusion with Anticodon Binding Domain of GluRS is Not Sufficient to Alter the Substrate Specificity of a Chimeric Glu-Q-RS.}, author = {S Ray and M Blaise and B Roy and S Ghosh and D Kern and R Banerjee}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24374508}, doi = {10.1007/s10930-013-9537-7}, isbn = {24374508}, year = {2014}, date = {2014-01-01}, journal = {Protein J}, volume = {33}, number = {1}, pages = {48-60}, abstract = {Glutamyl-queuosine-tRNAAsp synthetase (Glu-Q-RS) is a paralog of glutamyl-tRNA synthetase (GluRS) and is found in more than forty species of proteobacteria, cyanobacteria, and actinobacteria. Glu-Q-RS shows striking structural similarity with N-terminal catalytic domain of GluRS (NGluRS) but it lacks the C-terminal anticodon binding domain (CGluRS). In spite of structural similarities, Glu-Q-RS and NGluRS differ in their functional properties. Glu-Q-RS glutamylates the Q34 nucleotide of the anticodon of tRNAAsp whereas NGluRS constitutes the catalytic domain of GluRS catalyzing the transfer of Glu on the acceptor end of tRNAGlu. Since NGluRS is able to catalyze aminoacylation of only tRNAGlu the glutamylation capacity of tRNAAsp by Glu-Q-RS is surprising. To understand the substrate specificity of Glu-Q-RS we undertook a systemic approach by investigating the biophysical and biochemical properties of the NGluRS (1-301), CGluRS (314-471) and Glu-Q-RS-CGluRS, (1-298 of Glu-Q-RS fused to 314-471 from GluRS). Circular dichroism, fluorescence spectroscopy and differential scanning calorimetry analyses revealed absence of N-terminal domain (1-298 of Glu-Q-RS) and C-terminal domain (314-471 from GluRS) communication in chimera, in contrast to the native full length GluRS. The chimeric Glu-Q-RS is still able to aminoacylate tRNAAsp but has also the capacity to bind tRNAGlu. However the chimeric protein is unable to aminoacylate tRNAGlu probably as a consequence of the lack of domain-domain communication.}, keywords = {ERIANI, Unité ARN}, pubstate = {published}, tppubtype = {article} } Glutamyl-queuosine-tRNAAsp synthetase (Glu-Q-RS) is a paralog of glutamyl-tRNA synthetase (GluRS) and is found in more than forty species of proteobacteria, cyanobacteria, and actinobacteria. Glu-Q-RS shows striking structural similarity with N-terminal catalytic domain of GluRS (NGluRS) but it lacks the C-terminal anticodon binding domain (CGluRS). In spite of structural similarities, Glu-Q-RS and NGluRS differ in their functional properties. Glu-Q-RS glutamylates the Q34 nucleotide of the anticodon of tRNAAsp whereas NGluRS constitutes the catalytic domain of GluRS catalyzing the transfer of Glu on the acceptor end of tRNAGlu. Since NGluRS is able to catalyze aminoacylation of only tRNAGlu the glutamylation capacity of tRNAAsp by Glu-Q-RS is surprising. To understand the substrate specificity of Glu-Q-RS we undertook a systemic approach by investigating the biophysical and biochemical properties of the NGluRS (1-301), CGluRS (314-471) and Glu-Q-RS-CGluRS, (1-298 of Glu-Q-RS fused to 314-471 from GluRS). Circular dichroism, fluorescence spectroscopy and differential scanning calorimetry analyses revealed absence of N-terminal domain (1-298 of Glu-Q-RS) and C-terminal domain (314-471 from GluRS) communication in chimera, in contrast to the native full length GluRS. The chimeric Glu-Q-RS is still able to aminoacylate tRNAAsp but has also the capacity to bind tRNAGlu. However the chimeric protein is unable to aminoacylate tRNAGlu probably as a consequence of the lack of domain-domain communication. |
Ray, S; Banerjee, V; Blaise, M; Banerjee, B; Das, K P; Kern, D; Banerjee, R Critical Role of Zinc Ion on E. coli Glutamyl-Queuosine-tRNAAsp Synthetase (Glu-Q-RS) Structure and Function. Article de journal Protein J, 33 (2), p. 143-149, 2014, ISBN: 24505021. Résumé | Liens | BibTeX | Étiquettes: ERIANI, Unité ARN @article{, title = {Critical Role of Zinc Ion on E. coli Glutamyl-Queuosine-tRNA^{Asp} Synthetase (Glu-Q-RS) Structure and Function.}, author = {S Ray and V Banerjee and M Blaise and B Banerjee and K P Das and D Kern and R Banerjee}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24505021?dopt=Abstract}, doi = {10.1007/s10930-014-9546-1}, isbn = {24505021}, year = {2014}, date = {2014-01-01}, journal = {Protein J}, volume = {33}, number = {2}, pages = {143-149}, abstract = {Glutamyl-queuosine-tRNAAsp synthetase (Glu-Q-RS) and glutamyl-tRNA synthetase (GluRS), differ widely by their function although they share close structural resemblance within their catalytic core of GluRS. In particular both Escherichia coli GluRS and Glu-Q-RS contain a single zinc-binding site in their putative tRNA acceptor stem-binding domain. It has been shown that the zinc is crucial for correct positioning of the tRNAGlu acceptor-end in the active site of E. coli GluRS. To address the role of zinc ion in Glu-Q-RS, the C101S/C103S Glu-Q-RS variant is constructed. Energy dispersive X-ray fluorescence show that the zinc ion still remained coordinated but the variant became structurally labile and acquired aggregation capacity. The extent of aggregation of the protein is significantly decreased in presence of the small substrates and more particularly by adenosine triphosphate. Addition of zinc increased significantly the solubility of the variant. The aminoacylation assay reveals a decrease in activity of the variant even after addition of zinc as compared to the wild-type, although the secondary structure of the protein is not altered as shown by the Fourier transform infrared spectroscopy study.}, keywords = {ERIANI, Unité ARN}, pubstate = {published}, tppubtype = {article} } Glutamyl-queuosine-tRNAAsp synthetase (Glu-Q-RS) and glutamyl-tRNA synthetase (GluRS), differ widely by their function although they share close structural resemblance within their catalytic core of GluRS. In particular both Escherichia coli GluRS and Glu-Q-RS contain a single zinc-binding site in their putative tRNA acceptor stem-binding domain. It has been shown that the zinc is crucial for correct positioning of the tRNAGlu acceptor-end in the active site of E. coli GluRS. To address the role of zinc ion in Glu-Q-RS, the C101S/C103S Glu-Q-RS variant is constructed. Energy dispersive X-ray fluorescence show that the zinc ion still remained coordinated but the variant became structurally labile and acquired aggregation capacity. The extent of aggregation of the protein is significantly decreased in presence of the small substrates and more particularly by adenosine triphosphate. Addition of zinc increased significantly the solubility of the variant. The aminoacylation assay reveals a decrease in activity of the variant even after addition of zinc as compared to the wild-type, although the secondary structure of the protein is not altered as shown by the Fourier transform infrared spectroscopy study. |
Nowakowska, M; Kowalska, J; Martin, F; d'Orchymont, A; Zuberek, J; Lukaszewicz, M; Darzynkiewicz, E; Jemielity, J Cap analogs containing 6-thioguanosine - reagents for the synthesis of mRNAs selectively photo-crosslinkable with cap-binding biomolecules. Article de journal Org Biomol Chem, 12 (27), p. 4841-4847, 2014, ISBN: 24763507. Résumé | Liens | BibTeX | Étiquettes: ERIANI, Unité ARN @article{, title = {Cap analogs containing 6-thioguanosine - reagents for the synthesis of mRNAs selectively photo-crosslinkable with cap-binding biomolecules.}, author = {M Nowakowska and J Kowalska and F Martin and A d'Orchymont and J Zuberek and M Lukaszewicz and E Darzynkiewicz and J Jemielity}, url = {http://www.ncbi.nlm.nih.gov/pubmed/24763507}, doi = {10.1039/c4ob00059e}, isbn = {24763507}, year = {2014}, date = {2014-01-01}, journal = {Org Biomol Chem}, volume = {12}, number = {27}, pages = {4841-4847}, abstract = {Numerous biomolecules recognize the 7-methylguanosine cap structure present at the 5' ends of eukaryotic mRNAs. Photo-crosslinking is a valuable technique to study these interactions. We report three anti-reverse cap analogs containing a photo-activable nucleoside, 6-thioguanosine (6SG), that enable the synthesis of capped RNAs with 6SG positioned exclusively as the first transcribed nucleotide. The effect of the 6-thioguanosine moiety on binding to the translation factor eIF4E and the efficiency of mRNA translation was determined. The utility of mRNAs with a 6SG-modified cap in crosslinking experiments is shown by mapping the histone H4 cap-binding pocket.}, keywords = {ERIANI, Unité ARN}, pubstate = {published}, tppubtype = {article} } Numerous biomolecules recognize the 7-methylguanosine cap structure present at the 5' ends of eukaryotic mRNAs. Photo-crosslinking is a valuable technique to study these interactions. We report three anti-reverse cap analogs containing a photo-activable nucleoside, 6-thioguanosine (6SG), that enable the synthesis of capped RNAs with 6SG positioned exclusively as the first transcribed nucleotide. The effect of the 6-thioguanosine moiety on binding to the translation factor eIF4E and the efficiency of mRNA translation was determined. The utility of mRNAs with a 6SG-modified cap in crosslinking experiments is shown by mapping the histone H4 cap-binding pocket. |
Zhou, X L; Ruan, Z R; Wang, M; Fang, Z P; Wang, Y; Chen, Y; Liu, R J; Eriani, G; Wang, E D A minimalist mitochondrial threonyl-tRNA synthetase exhibits tRNA-isoacceptor specificity during proofreading. Article de journal Nucleic Acids Res, 42 (22), p. 13873-13886, 2014, ISBN: 25414329. Résumé | Liens | BibTeX | Étiquettes: ERIANI, Unité ARN @article{, title = {A minimalist mitochondrial threonyl-tRNA synthetase exhibits tRNA-isoacceptor specificity during proofreading.}, author = {X L Zhou and Z R Ruan and M Wang and Z P Fang and Y Wang and Y Chen and R J Liu and G Eriani and E D Wang}, url = {http://www.ncbi.nlm.nih.gov/pubmed/25414329?dopt=Abstract}, doi = {10.1093/nar/gku1218}, isbn = {25414329}, year = {2014}, date = {2014-01-01}, journal = {Nucleic Acids Res}, volume = {42}, number = {22}, pages = {13873-13886}, abstract = {Yeast mitochondria contain a minimalist threonyl-tRNA synthetase (ThrRS) composed only of the catalytic core and tRNA binding domain but lacking the entire editing domain. Besides the usual tRNAThr2, some budding yeasts, such as Saccharomyces cerevisiae, also contain a non-canonical tRNAThr1 with an enlarged 8-nucleotide anticodon loop, reprograming the usual leucine CUN codons to threonine. This raises interesting questions about the aminoacylation fidelity of such ThrRSs and the possible contribution of the two tRNAThrs during editing. Here, we found that, despite the absence of the editing domain, S. cerevisiae mitochondrial ThrRS (ScmtThrRS) harbors a tRNA-dependent pre-transfer editing activity. Remarkably, only the usual tRNAThr2 stimulated pre-transfer editing, thus, establishing the first example of a synthetase exhibiting tRNA-isoacceptor specificity during pre-transfer editing. We also showed that the failure of tRNAThr1 to stimulate tRNA-dependent pre-transfer editing was due to the lack of an editing domain. Using assays of the complementation of a ScmtThrRS gene knockout strain, we showed that the catalytic core and tRNA binding domain of ScmtThrRS co-evolved to recognize the unusual tRNAThr1. In combination, the results provide insights into the tRNA-dependent editing process and suggest that tRNA-dependent pre-transfer editing takes place in the aminoacylation catalytic core.}, keywords = {ERIANI, Unité ARN}, pubstate = {published}, tppubtype = {article} } Yeast mitochondria contain a minimalist threonyl-tRNA synthetase (ThrRS) composed only of the catalytic core and tRNA binding domain but lacking the entire editing domain. Besides the usual tRNAThr2, some budding yeasts, such as Saccharomyces cerevisiae, also contain a non-canonical tRNAThr1 with an enlarged 8-nucleotide anticodon loop, reprograming the usual leucine CUN codons to threonine. This raises interesting questions about the aminoacylation fidelity of such ThrRSs and the possible contribution of the two tRNAThrs during editing. Here, we found that, despite the absence of the editing domain, S. cerevisiae mitochondrial ThrRS (ScmtThrRS) harbors a tRNA-dependent pre-transfer editing activity. Remarkably, only the usual tRNAThr2 stimulated pre-transfer editing, thus, establishing the first example of a synthetase exhibiting tRNA-isoacceptor specificity during pre-transfer editing. We also showed that the failure of tRNAThr1 to stimulate tRNA-dependent pre-transfer editing was due to the lack of an editing domain. Using assays of the complementation of a ScmtThrRS gene knockout strain, we showed that the catalytic core and tRNA binding domain of ScmtThrRS co-evolved to recognize the unusual tRNAThr1. In combination, the results provide insights into the tRNA-dependent editing process and suggest that tRNA-dependent pre-transfer editing takes place in the aminoacylation catalytic core. |
2012 |
Martin, F Fifteen years of the yeast three-hybrid system: RNA-protein interactions under investigation. Article de journal Methods, 58 (4), p. 367-375, 2012, ISBN: 2284156. Résumé | Liens | BibTeX | Étiquettes: ERIANI, Unité ARN @article{, title = {Fifteen years of the yeast three-hybrid system: RNA-protein interactions under investigation.}, author = {F Martin}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22841566?dopt=Abstract}, doi = {10.1016/j.ymeth.2012.07.016}, isbn = {2284156}, year = {2012}, date = {2012-01-01}, journal = {Methods}, volume = {58}, number = {4}, pages = {367-375}, abstract = {In 1996, the Wickens and the Kuhl labs developed the yeast three-hybrid system independently. By expressing two chimeric proteins and one chimeric RNA molecule in Saccharomyces cerevisiae, this method allows in vivo monitoring of RNA-protein interactions by measuring the expression levels of HIS3 and LacZ reporter genes. Specific RNA targets have been used to characterize unknown RNA binding proteins. Previously described RNA binding proteins have also been used as bait to select new RNA targets. Finally, this method has been widely used to investigate or confirm previously suspected RNA-protein interactions. However, this method falls short in some aspects, such as RNA display and selection of false positive molecules. This review will summarize the results obtained with this method from the past 15years, as well as on recent efforts to improve its specificity.}, keywords = {ERIANI, Unité ARN}, pubstate = {published}, tppubtype = {article} } In 1996, the Wickens and the Kuhl labs developed the yeast three-hybrid system independently. By expressing two chimeric proteins and one chimeric RNA molecule in Saccharomyces cerevisiae, this method allows in vivo monitoring of RNA-protein interactions by measuring the expression levels of HIS3 and LacZ reporter genes. Specific RNA targets have been used to characterize unknown RNA binding proteins. Previously described RNA binding proteins have also been used as bait to select new RNA targets. Finally, this method has been widely used to investigate or confirm previously suspected RNA-protein interactions. However, this method falls short in some aspects, such as RNA display and selection of false positive molecules. This review will summarize the results obtained with this method from the past 15years, as well as on recent efforts to improve its specificity. |
Huang, Q; Yao, P; Eriani, G; Wang, E D In vivo identification of essential nucleotides in tRNALeu to its functions by using a constructed yeast tRNALeu knockout strain. Article de journal Nucleic Acids Res, 40 (20), p. 10463-10477, 2012, ISBN: 22917587. Résumé | Liens | BibTeX | Étiquettes: ERIANI, Unité ARN @article{, title = {In vivo identification of essential nucleotides in tRNALeu to its functions by using a constructed yeast tRNALeu knockout strain.}, author = {Q Huang and P Yao and G Eriani and E D Wang}, url = {http://www.ncbi.nlm.nih.gov/pubmed/22917587?dopt=Abstract}, doi = {10.1093/nar/gks783}, isbn = {22917587}, year = {2012}, date = {2012-01-01}, journal = {Nucleic Acids Res}, volume = {40}, number = {20}, pages = {10463-10477}, abstract = {The fidelity of protein biosynthesis requires the aminoacylation of tRNA with its cognate amino acid catalyzed by aminoacyl-tRNA synthetase with high levels of accuracy and efficiency. Crucial bases in tRNA(Leu) to aminoacylation or editing functions of leucyl-tRNA synthetase have been extensively studied mainly by in vitro methods. In the present study, we constructed two Saccharomyces cerevisiae tRNA(Leu) knockout strains carrying deletions of the genes for tRNA(Leu)(GAG) and tRNA(Leu)(UAG). Disrupting the single gene encoding tRNA(Leu)(GAG) had no phenotypic consequence when compared to the wild-type strain. While disrupting the three genes for tRNA(Leu)(UAG) had a lethal effect on the yeast strain, indicating that tRNA(Leu)(UAG) decoding capacity could not be compensated by another tRNA(Leu) isoacceptor. Using the triple tRNA knockout strain and a randomly mutated library of tRNA(Leu)(UAG), a selection to identify critical tRNA(Leu) elements was performed. In this way, mutations inducing in vivo decreases of tRNA levels or aminoacylation or editing ability by leucyl-tRNA synthetase were identified. Overall, the data showed that the triple tRNA knockout strain is a suitable tool for in vivo studies and identification of essential nucleotides of the tRNA.}, keywords = {ERIANI, Unité ARN}, pubstate = {published}, tppubtype = {article} } The fidelity of protein biosynthesis requires the aminoacylation of tRNA with its cognate amino acid catalyzed by aminoacyl-tRNA synthetase with high levels of accuracy and efficiency. Crucial bases in tRNA(Leu) to aminoacylation or editing functions of leucyl-tRNA synthetase have been extensively studied mainly by in vitro methods. In the present study, we constructed two Saccharomyces cerevisiae tRNA(Leu) knockout strains carrying deletions of the genes for tRNA(Leu)(GAG) and tRNA(Leu)(UAG). Disrupting the single gene encoding tRNA(Leu)(GAG) had no phenotypic consequence when compared to the wild-type strain. While disrupting the three genes for tRNA(Leu)(UAG) had a lethal effect on the yeast strain, indicating that tRNA(Leu)(UAG) decoding capacity could not be compensated by another tRNA(Leu) isoacceptor. Using the triple tRNA knockout strain and a randomly mutated library of tRNA(Leu)(UAG), a selection to identify critical tRNA(Leu) elements was performed. In this way, mutations inducing in vivo decreases of tRNA levels or aminoacylation or editing ability by leucyl-tRNA synthetase were identified. Overall, the data showed that the triple tRNA knockout strain is a suitable tool for in vivo studies and identification of essential nucleotides of the tRNA. |
2011 |
Rudinger-Thirion, J; Lescure, A; Paulus, C; Frugier, M Misfolded human tRNA isodecoder binds and neutralizes a 3' UTR-embedded Alu element Article de journal Proc Natl Acad Sci U S A, 108 (40), p. E794-802, 2011, ISSN: 1091-6490 (Electronic) 0027-8424 (Linking), (Rudinger-Thirion, Joelle Lescure, Alain Paulus, Caroline Frugier, Magali United States Proceedings of the National Academy of Sciences of the United States of America Proc Natl Acad Sci U S A. 2011 Oct 4;108(40):E794-802. Epub 2011 Sep 6.). Résumé | Liens | BibTeX | Étiquettes: ERIANI, FRUGIER, LESCURE, Unité ARN @article{, title = {Misfolded human tRNA isodecoder binds and neutralizes a 3' UTR-embedded Alu element}, author = {J Rudinger-Thirion and A Lescure and C Paulus and M Frugier}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=21896722}, doi = {10.1073/pnas.1103698108}, issn = {1091-6490 (Electronic) 0027-8424 (Linking)}, year = {2011}, date = {2011-01-01}, journal = {Proc Natl Acad Sci U S A}, volume = {108}, number = {40}, pages = {E794-802}, abstract = {Several classes of small noncoding RNAs are key players in cellular metabolism including mRNA decoding, RNA processing, and mRNA stability. Here we show that a tRNA(Asp) isodecoder, corresponding to a human tRNA-derived sequence, binds to an embedded Alu RNA element contained in the 3' UTR of the human aspartyl-tRNA synthetase mRNA. This interaction between two well-known classes of RNA molecules, tRNA and Alu RNA, is driven by an unexpected structural motif and induces a global rearrangement of the 3' UTR. Besides, this 3' UTR contains two functional polyadenylation signals. We propose a model where the tRNA/Alu interaction would modulate the accessibility of the two alternative polyadenylation sites and regulate the stability of the mRNA. This unique regulation mechanism would link gene expression to RNA polymerase III transcription and may have implications in a primate-specific signal pathway.}, note = {Rudinger-Thirion, Joelle Lescure, Alain Paulus, Caroline Frugier, Magali United States Proceedings of the National Academy of Sciences of the United States of America Proc Natl Acad Sci U S A. 2011 Oct 4;108(40):E794-802. Epub 2011 Sep 6.}, keywords = {ERIANI, FRUGIER, LESCURE, Unité ARN}, pubstate = {published}, tppubtype = {article} } Several classes of small noncoding RNAs are key players in cellular metabolism including mRNA decoding, RNA processing, and mRNA stability. Here we show that a tRNA(Asp) isodecoder, corresponding to a human tRNA-derived sequence, binds to an embedded Alu RNA element contained in the 3' UTR of the human aspartyl-tRNA synthetase mRNA. This interaction between two well-known classes of RNA molecules, tRNA and Alu RNA, is driven by an unexpected structural motif and induces a global rearrangement of the 3' UTR. Besides, this 3' UTR contains two functional polyadenylation signals. We propose a model where the tRNA/Alu interaction would modulate the accessibility of the two alternative polyadenylation sites and regulate the stability of the mRNA. This unique regulation mechanism would link gene expression to RNA polymerase III transcription and may have implications in a primate-specific signal pathway. |
Zhou, X L; Du, D H; Tan, M; Lei, H Y; Ruan, L L; Eriani, G; Wang, E D Role of tRNA amino acid-accepting end in aminoacylation and its quality control Article de journal Nucleic Acids Res, 39 (20), p. 8857-8868, 2011, ISSN: 1362-4962 (Electronic) 0305-1048 (Linking), (DOI: 10.1093/nar/gkr595). Résumé | Liens | BibTeX | Étiquettes: ERIANI, Unité ARN @article{, title = {Role of tRNA amino acid-accepting end in aminoacylation and its quality control}, author = {X L Zhou and D H Du and M Tan and H Y Lei and L L Ruan and G Eriani and E D Wang}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=21775341}, doi = {10.1093/nar/gkr595}, issn = {1362-4962 (Electronic) 0305-1048 (Linking)}, year = {2011}, date = {2011-01-01}, journal = {Nucleic Acids Res}, volume = {39}, number = {20}, pages = {8857-8868}, abstract = {Aminoacyl-tRNA synthetases (aaRSs) are remarkable enzymes that are in charge of the accurate recognition and ligation of amino acids and tRNA molecules. The greatest difficulty in accurate aminoacylation appears to be in discriminating between highly similar amino acids. To reduce mischarging of tRNAs by non-cognate amino acids, aaRSs have evolved an editing activity in a second active site to cleave the incorrect aminoacyl-tRNAs. Editing occurs after translocation of the aminoacyl-CCA(76) end to the editing site, switching between a hairpin and a helical conformation for aminoacylation and editing. Here, we studied the consequence of nucleotide changes in the CCA(76) accepting end of tRNA(Leu) during the aminoacylation and editing reactions. The analysis showed that the terminal A(76) is essential for both reactions, suggesting that critical interactions occur in the two catalytic sites. Substitutions of C(74) and C(75) selectively decreased aminoacylation keeping nearly unaffected editing. These mutations might favor the regular helical conformation required to reach the editing site. Mutating the editing domain residues that contribute to CCA(76) binding reduced the aminoacylation fidelity leading to cell-toxicity in the presence of non-cognate amino acids. Collectively, the data show how protein synthesis quality is controlled by the CCA(76) homogeneity of tRNAs.}, note = {DOI: 10.1093/nar/gkr595}, keywords = {ERIANI, Unité ARN}, pubstate = {published}, tppubtype = {article} } Aminoacyl-tRNA synthetases (aaRSs) are remarkable enzymes that are in charge of the accurate recognition and ligation of amino acids and tRNA molecules. The greatest difficulty in accurate aminoacylation appears to be in discriminating between highly similar amino acids. To reduce mischarging of tRNAs by non-cognate amino acids, aaRSs have evolved an editing activity in a second active site to cleave the incorrect aminoacyl-tRNAs. Editing occurs after translocation of the aminoacyl-CCA(76) end to the editing site, switching between a hairpin and a helical conformation for aminoacylation and editing. Here, we studied the consequence of nucleotide changes in the CCA(76) accepting end of tRNA(Leu) during the aminoacylation and editing reactions. The analysis showed that the terminal A(76) is essential for both reactions, suggesting that critical interactions occur in the two catalytic sites. Substitutions of C(74) and C(75) selectively decreased aminoacylation keeping nearly unaffected editing. These mutations might favor the regular helical conformation required to reach the editing site. Mutating the editing domain residues that contribute to CCA(76) binding reduced the aminoacylation fidelity leading to cell-toxicity in the presence of non-cognate amino acids. Collectively, the data show how protein synthesis quality is controlled by the CCA(76) homogeneity of tRNAs. |
2009 |
Bour, T; Akaddar, A; Lorber, B; Blais, S; Balg, C; Candolfi, E; Frugier, M Plasmodial aspartyl-tRNA synthetases and peculiarities in Plasmodium falciparum Article de journal J Biol Chem, 284 (28), p. 18893-18903, 2009, ISBN: 19443655, (0021-9258 (Print) 0021-9258 (Linking) Journal Article Research Support, Non-U.S. Gov't). Résumé | Liens | BibTeX | Étiquettes: Amino Acid, ERIANI, FRUGIER, FRUGIER FLORENTZ Amino Acid Sequence Amino Acids/chemistry Animals Aspartate-tRNA Ligase/*metabolism Aspartic Acid/chemistry Base Sequence Cloning, Molecular Cytoplasm/metabolism Dimerization Fungal Proteins/chemistry Humans Kinetics Molecular Sequence Data Plasmodium falciparum Protein Structure, Tertiary Sequence Homology, Unité ARN @article{, title = {Plasmodial aspartyl-tRNA synthetases and peculiarities in Plasmodium falciparum}, author = {T Bour and A Akaddar and B Lorber and S Blais and C Balg and E Candolfi and M Frugier}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19443655}, isbn = {19443655}, year = {2009}, date = {2009-01-01}, journal = {J Biol Chem}, volume = {284}, number = {28}, pages = {18893-18903}, abstract = {Distinctive features of aspartyl-transfer RNA (tRNA) synthetases (AspRS) from the protozoan Plasmodium genus are described. These apicomplexan AspRSs contain 29-31 amino acid insertions in their anticodon binding domains, a remarkably long N-terminal appendix that varies in size from 110 to 165 amino acids and two potential initiation codons. This article focuses on the atypical functional and structural properties of Plasmodium falciparum cytosolic AspRS, the causative parasite of human malaria. This species encodes a 626 or 577 amino acids AspRS depending on whether initiation starts on the first or second in-frame initiation codon. The longer protein has poor solubility and a propensity to aggregate. Production of the short version was favored as shown by the comparison of the recombinant protein with endogenous AspRS. Comparison of the tRNA aminoacylation activity of wild-type and mutant parasite AspRSs with those of yeast and human AspRSs revealed unique properties. The N-terminal extension contains a motif that provides unexpectedly strong RNA binding to plasmodial AspRS. Furthermore, experiments demonstrated the requirement of the plasmodial insertion for AspRS dimerization and, therefore, tRNA aminoacylation and other putative functions. Implications for the parasite biology are proposed. These data provide a robust background for unraveling the precise functional properties of the parasite AspRS and for developing novel lead compounds against malaria, targeting its idiosyncratic domains.}, note = {0021-9258 (Print) 0021-9258 (Linking) Journal Article Research Support, Non-U.S. Gov't}, keywords = {Amino Acid, ERIANI, FRUGIER, FRUGIER FLORENTZ Amino Acid Sequence Amino Acids/chemistry Animals Aspartate-tRNA Ligase/*metabolism Aspartic Acid/chemistry Base Sequence Cloning, Molecular Cytoplasm/metabolism Dimerization Fungal Proteins/chemistry Humans Kinetics Molecular Sequence Data Plasmodium falciparum Protein Structure, Tertiary Sequence Homology, Unité ARN}, pubstate = {published}, tppubtype = {article} } Distinctive features of aspartyl-transfer RNA (tRNA) synthetases (AspRS) from the protozoan Plasmodium genus are described. These apicomplexan AspRSs contain 29-31 amino acid insertions in their anticodon binding domains, a remarkably long N-terminal appendix that varies in size from 110 to 165 amino acids and two potential initiation codons. This article focuses on the atypical functional and structural properties of Plasmodium falciparum cytosolic AspRS, the causative parasite of human malaria. This species encodes a 626 or 577 amino acids AspRS depending on whether initiation starts on the first or second in-frame initiation codon. The longer protein has poor solubility and a propensity to aggregate. Production of the short version was favored as shown by the comparison of the recombinant protein with endogenous AspRS. Comparison of the tRNA aminoacylation activity of wild-type and mutant parasite AspRSs with those of yeast and human AspRSs revealed unique properties. The N-terminal extension contains a motif that provides unexpectedly strong RNA binding to plasmodial AspRS. Furthermore, experiments demonstrated the requirement of the plasmodial insertion for AspRS dimerization and, therefore, tRNA aminoacylation and other putative functions. Implications for the parasite biology are proposed. These data provide a robust background for unraveling the precise functional properties of the parasite AspRS and for developing novel lead compounds against malaria, targeting its idiosyncratic domains. |
Zhu, B; Yao, P; Tan, M; Eriani, G; Wang, E D tRNA-independent Pretransfer Editing by Class I Leucyl-tRNA Synthetase Article de journal J Biol Chem, 284 (6), p. 3418-3424, 2009, ISBN: 19068478, (0021-9258 (Print) Journal Article). Résumé | Liens | BibTeX | Étiquettes: ERIANI, Unité ARN @article{, title = {tRNA-independent Pretransfer Editing by Class I Leucyl-tRNA Synthetase}, author = {B Zhu and P Yao and M Tan and G Eriani and E D Wang}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19068478}, isbn = {19068478}, year = {2009}, date = {2009-01-01}, journal = {J Biol Chem}, volume = {284}, number = {6}, pages = {3418-3424}, abstract = {Aminoacyl-tRNA synthetases catalyze the formation of aminoacyl-tRNA in a two-step reaction starting with amino acid activation followed by aminoacyl group transfer to tRNA. To clear mistakes that occasionally occur, some of these enzymes carry out editing activities, acting on the misactivated amino acid (pretransfer editing) or after the transfer on the tRNA (post-transfer editing). The post-transfer editing pathway of leucyl-tRNA synthetase has been extensively studied by structural and biochemical approaches. Here, we report the finding of a tRNA-independent pretransfer editing pathway in leucyl-tRNA synthetases from Aquifex aeolicus. Using a CP1-mutant defective in its post-transfer editing function, we showed that this new editing pathway is distinct from the post-transfer editing site and may occur at the synthetic catalytic site, as recently proposed for other aminoacyl-tRNA synthetases.}, note = {0021-9258 (Print) Journal Article}, keywords = {ERIANI, Unité ARN}, pubstate = {published}, tppubtype = {article} } Aminoacyl-tRNA synthetases catalyze the formation of aminoacyl-tRNA in a two-step reaction starting with amino acid activation followed by aminoacyl group transfer to tRNA. To clear mistakes that occasionally occur, some of these enzymes carry out editing activities, acting on the misactivated amino acid (pretransfer editing) or after the transfer on the tRNA (post-transfer editing). The post-transfer editing pathway of leucyl-tRNA synthetase has been extensively studied by structural and biochemical approaches. Here, we report the finding of a tRNA-independent pretransfer editing pathway in leucyl-tRNA synthetases from Aquifex aeolicus. Using a CP1-mutant defective in its post-transfer editing function, we showed that this new editing pathway is distinct from the post-transfer editing site and may occur at the synthetic catalytic site, as recently proposed for other aminoacyl-tRNA synthetases. |
Giege, R; Eriani, G Transfer RNA recognition by synthetases Book Chapter Encyclopedia of Life Sciences, John Wiley & Sons, 2009. Résumé | Liens | BibTeX | Étiquettes: ERIANI, ERIANI GIEGE Aminoacyl-tRNA synthetase Genetic code Protein synthesis RNA recognition tRNA, Unité ARN @inbook{, title = {Transfer RNA recognition by synthetases}, author = {R Giege and G Eriani}, url = {http://www.els.net/WileyCDA/ElsArticle/refId-a0000531.html}, doi = {10.1002/9780470015902.a0000531.pub2}, year = {2009}, date = {2009-01-01}, booktitle = {Encyclopedia of Life Sciences}, publisher = {John Wiley & Sons}, abstract = {Fidelity of transfer ribonucleic acid (tRNA) charging by amino acids ensures correct translation of the genetic code into proteins. Charging is catalysed by a set of enzymes known as aminoacyl-tRNA synthetases. Owing to the degeneracy of the genetic code, some of the different tRNAs have the same amino acid attached to them. Specificity of the charging reaction is ensured by positive elements, the identity determinants unique to each tRNA and responsible for its recognition by the cognate synthetase, and negative elements, the antideterminants that prevent false recognitions. To fulfil the aminoacylation specificity and prevent noncognate aminoacyl-tRNA delivery to the ribosome, some synthetases also mediate proofreading reactions that increase fidelity of the tRNA charging. In such reactions, misactivated amino acids or mischarged tRNAs are checked in specific sites and noncognate products are hydrolysed.}, keywords = {ERIANI, ERIANI GIEGE Aminoacyl-tRNA synthetase Genetic code Protein synthesis RNA recognition tRNA, Unité ARN}, pubstate = {published}, tppubtype = {inbook} } Fidelity of transfer ribonucleic acid (tRNA) charging by amino acids ensures correct translation of the genetic code into proteins. Charging is catalysed by a set of enzymes known as aminoacyl-tRNA synthetases. Owing to the degeneracy of the genetic code, some of the different tRNAs have the same amino acid attached to them. Specificity of the charging reaction is ensured by positive elements, the identity determinants unique to each tRNA and responsible for its recognition by the cognate synthetase, and negative elements, the antideterminants that prevent false recognitions. To fulfil the aminoacylation specificity and prevent noncognate aminoacyl-tRNA delivery to the ribosome, some synthetases also mediate proofreading reactions that increase fidelity of the tRNA charging. In such reactions, misactivated amino acids or mischarged tRNAs are checked in specific sites and noncognate products are hydrolysed. |
2008 |
Ryckelynck, M; Paulus, C A; Frugier, M Post-Translational Modifications Guard Yeast from Misaspartylation Article de journal Biochemistry, 47 (47), p. 12476-12482, 2008, ISBN: 18956891, (1520-4995 (Electronic) 0006-2960 (Linking) Journal article). Résumé | Liens | BibTeX | Étiquettes: ERIANI, FRUGIER, RYCKELYNCK, Unité ARN @article{, title = {Post-Translational Modifications Guard Yeast from Misaspartylation}, author = {M Ryckelynck and C A Paulus and M Frugier}, url = {http://www.ncbi.nlm.nih.gov/pubmed/18956885}, isbn = {18956891}, year = {2008}, date = {2008-01-01}, journal = {Biochemistry}, volume = {47}, number = {47}, pages = {12476-12482}, abstract = {Yeast aspartyl-tRNA synthetase (AspRS) is downregulated at the post-transcriptional level. This complex retro-inhibition mechanism causes the cell to equilibrate cellular concentrations of tRNA (Asp), AspRS, and its encoding mRNA. This strategy hinders AspRS accumulation to keep misacylation of heterologous tRNAs under control. Here, the AspRS concentration was increased artificially in vivo but did not generate tRNA (Asn) and/or tRNA (Glu) misaspartylation or the logical consecutive post-translational stress. This work allowed the detection of an additional subtle cellular lock capable of blocking AspRS toxicity. This study revealed the presence of post-translational modifications in the N-terminal extension of AspRS. We hypothesize that by neutralizing the lysine-rich motif contained in this domain, the cell mobilizes an additional strategy that considerably reduces the probability of the enzyme binding and aspartylating noncognate tRNAs and thus harming its own translation.}, note = {1520-4995 (Electronic) 0006-2960 (Linking) Journal article}, keywords = {ERIANI, FRUGIER, RYCKELYNCK, Unité ARN}, pubstate = {published}, tppubtype = {article} } Yeast aspartyl-tRNA synthetase (AspRS) is downregulated at the post-transcriptional level. This complex retro-inhibition mechanism causes the cell to equilibrate cellular concentrations of tRNA (Asp), AspRS, and its encoding mRNA. This strategy hinders AspRS accumulation to keep misacylation of heterologous tRNAs under control. Here, the AspRS concentration was increased artificially in vivo but did not generate tRNA (Asn) and/or tRNA (Glu) misaspartylation or the logical consecutive post-translational stress. This work allowed the detection of an additional subtle cellular lock capable of blocking AspRS toxicity. This study revealed the presence of post-translational modifications in the N-terminal extension of AspRS. We hypothesize that by neutralizing the lysine-rich motif contained in this domain, the cell mobilizes an additional strategy that considerably reduces the probability of the enzyme binding and aspartylating noncognate tRNAs and thus harming its own translation. |
Yao, P; Zhu, B; Jaeger, S; Eriani, G; Wang, E D Recognition of tRNALeu by Aquifex aeolicus leucyl-tRNA synthetase during the aminoacylation and editing steps Article de journal Nucleic Acids Res, 36 (8), p. 2728-2738, 2008, ISBN: 18367476, (1362-4962 (Electronic) Journal Article Research Support, Non-U.S. Gov't). Résumé | Liens | BibTeX | Étiquettes: ERIANI, ERIANI Amino Acids/chemistry Anticodon/chemistry Bacteria/enzymology/genetics Base Sequence Iodine Leucine-tRNA Ligase/chemistry/*metabolism Molecular Sequence Data Mutagenesis Nucleic Acid Conformation Protein Footprinting RNA, Leu/*chemistry/genetics/metabolism Ribonucleases Substrate Specificity *Transfer RNA Aminoacylation, Transfer, Unité ARN @article{, title = {Recognition of tRNALeu by Aquifex aeolicus leucyl-tRNA synthetase during the aminoacylation and editing steps}, author = {P Yao and B Zhu and S Jaeger and G Eriani and E D Wang}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18367476}, isbn = {18367476}, year = {2008}, date = {2008-01-01}, journal = {Nucleic Acids Res}, volume = {36}, number = {8}, pages = {2728-2738}, abstract = {Recognition of tRNA by the cognate aminoacyl-tRNA synthetase during translation is crucial to ensure the correct expression of the genetic code. To understand tRNA(Leu) recognition sets and their evolution, the recognition of tRNA(Leu) by the leucyl-tRNA synthetase (LeuRS) from the primitive hyperthermophilic bacterium Aquifex aeolicus was studied by RNA probing and mutagenesis. The results show that the base A73; the core structure of tRNA formed by the tertiary interactions U8-A14, G18-U55 and G19-C56; and the orientation of the variable arm are critical elements for tRNA(Leu) aminoacylation. Although dispensable for aminoacylation, the anticodon arm carries discrete editing determinants that are required for stabilizing the conformation of the post-transfer editing state and for promoting translocation of the tRNA acceptor arm from the synthetic to the editing site.}, note = {1362-4962 (Electronic) Journal Article Research Support, Non-U.S. Gov't}, keywords = {ERIANI, ERIANI Amino Acids/chemistry Anticodon/chemistry Bacteria/enzymology/genetics Base Sequence Iodine Leucine-tRNA Ligase/chemistry/*metabolism Molecular Sequence Data Mutagenesis Nucleic Acid Conformation Protein Footprinting RNA, Leu/*chemistry/genetics/metabolism Ribonucleases Substrate Specificity *Transfer RNA Aminoacylation, Transfer, Unité ARN}, pubstate = {published}, tppubtype = {article} } Recognition of tRNA by the cognate aminoacyl-tRNA synthetase during translation is crucial to ensure the correct expression of the genetic code. To understand tRNA(Leu) recognition sets and their evolution, the recognition of tRNA(Leu) by the leucyl-tRNA synthetase (LeuRS) from the primitive hyperthermophilic bacterium Aquifex aeolicus was studied by RNA probing and mutagenesis. The results show that the base A73; the core structure of tRNA formed by the tertiary interactions U8-A14, G18-U55 and G19-C56; and the orientation of the variable arm are critical elements for tRNA(Leu) aminoacylation. Although dispensable for aminoacylation, the anticodon arm carries discrete editing determinants that are required for stabilizing the conformation of the post-transfer editing state and for promoting translocation of the tRNA acceptor arm from the synthetic to the editing site. |
2007 |
Zhu, B; Zhao, M W; Eriani, G; Wang, E D A present-day aminoacyl-tRNA synthetase with ancestral editing properties Article de journal RNA, 13 (1), p. 15-21, 2007, ISBN: 17095543, (1355-8382 (Print) Journal Article Research Support, Non-U.S. Gov't). Résumé | Liens | BibTeX | Étiquettes: ERIANI, Unité ARN @article{, title = {A present-day aminoacyl-tRNA synthetase with ancestral editing properties}, author = {B Zhu and M W Zhao and G Eriani and E D Wang}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17095543}, isbn = {17095543}, year = {2007}, date = {2007-01-01}, journal = {RNA}, volume = {13}, number = {1}, pages = {15-21}, abstract = {Leucyl-, isoleucyl-, and valyl-tRNA synthetases form a subgroup of related aminoacyl-tRNA synthetases that attach similar amino acids to their cognate tRNAs. To prevent amino acid misincorporation during translation, these enzymes also hydrolyze mischarged tRNAs through a post-transfer editing mechanism. Here we show that LeuRS from the deep-branching bacterium Aquifex aeolicus edits the complete set of aminoacylated tRNAs generated by the three enzymes: Ile-tRNA(Ile), Val-tRNA(Ile), Val-tRNA(Val), Thr-tRNA(Val), and Ile-tRNA(Leu). This unusual enlarged editing property was studied in a model of a primitive editing system containing a composite minihelix carrying the triple leucine, isoleucine, and valine identity mimicking the primitive tRNA precursor. We found that the freestanding LeuRS editing domain can edit this precursor in contrast to IleRS and ValRS editing domains. These results suggest that A. aeolicus LeuRS carries editing properties that seem more primitive than those of IleRS and ValRS. They suggest that the A. aeolicus editing domain has preserved the ambiguous editing property from the ancestral common editing domain or, alternatively, that this plasticity results from a specific metabolic adaptation.}, note = {1355-8382 (Print) Journal Article Research Support, Non-U.S. Gov't}, keywords = {ERIANI, Unité ARN}, pubstate = {published}, tppubtype = {article} } Leucyl-, isoleucyl-, and valyl-tRNA synthetases form a subgroup of related aminoacyl-tRNA synthetases that attach similar amino acids to their cognate tRNAs. To prevent amino acid misincorporation during translation, these enzymes also hydrolyze mischarged tRNAs through a post-transfer editing mechanism. Here we show that LeuRS from the deep-branching bacterium Aquifex aeolicus edits the complete set of aminoacylated tRNAs generated by the three enzymes: Ile-tRNA(Ile), Val-tRNA(Ile), Val-tRNA(Val), Thr-tRNA(Val), and Ile-tRNA(Leu). This unusual enlarged editing property was studied in a model of a primitive editing system containing a composite minihelix carrying the triple leucine, isoleucine, and valine identity mimicking the primitive tRNA precursor. We found that the freestanding LeuRS editing domain can edit this precursor in contrast to IleRS and ValRS editing domains. These results suggest that A. aeolicus LeuRS carries editing properties that seem more primitive than those of IleRS and ValRS. They suggest that the A. aeolicus editing domain has preserved the ambiguous editing property from the ancestral common editing domain or, alternatively, that this plasticity results from a specific metabolic adaptation. |
2006 |
Olieric, N; Bey, G; Nierengarten, H; Wang, E D; Moras, D; Eriani, G; Cavarelli, J Expression, purification, and characterization of a new heterotetramer structure of leucyl-tRNA synthetase from Aquifex aeolicus in Escherichia coli Article de journal Protein Expr Purif, 47 (1), p. 1-9, 2006, ISBN: 16256368, (1046-5928 (Print) Journal Article). Résumé | Liens | BibTeX | Étiquettes: DUMAS ERIANI, ERIANI, Unité ARN @article{, title = {Expression, purification, and characterization of a new heterotetramer structure of leucyl-tRNA synthetase from Aquifex aeolicus in Escherichia coli}, author = {N Olieric and G Bey and H Nierengarten and E D Wang and D Moras and G Eriani and J Cavarelli}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16256368}, isbn = {16256368}, year = {2006}, date = {2006-01-01}, journal = {Protein Expr Purif}, volume = {47}, number = {1}, pages = {1-9}, abstract = {Aminoacyl-tRNA synthetases are key players in the interpretation of the genetic code. They constitute a textbook example of multi-domain proteins including insertion and terminal functional modules appended to one of the two class-specific active site domains. The non-catalytic domains usually have distinct roles in the aminoacylation reaction. Aquifex aeolicus leucyl-tRNA synthetase (LeuRS) is composed of a separated catalytic site and tRNA anticodon-binding site, which would represent one of the closest relics of the primordial aminoacyl-tRNA synthetase. Moreover, the essential catalytic site residues are split into the two different subunits. In all other class-I aminoacyl-tRNA synthetases, those two functional polypeptides are nowadays fused into a single protein chain. In this work, we report the isolation and the characterization, in Escherichia coli, of a novel oligomeric form (alphabeta)2 for A. aeolicus LeuRS, which is present in addition to the alphabeta heterodimer. A. aeolicus (alphabeta)2 LeuRS has been characterized by biochemical and biophysical methods. Native gel electrophoresis, mass spectrometry, analytical ultracentrifugation, and kinetic analysis confirmed that the (alphabeta)2 enzyme was a stable and active entity. By mass spectrometry we confirmed that the heterodimer alphabeta can bind one tRNALeu molecule whereas the heterotetramer (alphabeta)2 can bind two tRNALeu molecules. Active site titration and aminoacylation assays showed that two functional active sites are found per heterotetramer, suggesting that this molecular species might exist and be active in vivo. All those data suggest that the existence of the heterotetramer is certainly not an artifact of overexpression in E. coli.}, note = {1046-5928 (Print) Journal Article}, keywords = {DUMAS ERIANI, ERIANI, Unité ARN}, pubstate = {published}, tppubtype = {article} } Aminoacyl-tRNA synthetases are key players in the interpretation of the genetic code. They constitute a textbook example of multi-domain proteins including insertion and terminal functional modules appended to one of the two class-specific active site domains. The non-catalytic domains usually have distinct roles in the aminoacylation reaction. Aquifex aeolicus leucyl-tRNA synthetase (LeuRS) is composed of a separated catalytic site and tRNA anticodon-binding site, which would represent one of the closest relics of the primordial aminoacyl-tRNA synthetase. Moreover, the essential catalytic site residues are split into the two different subunits. In all other class-I aminoacyl-tRNA synthetases, those two functional polypeptides are nowadays fused into a single protein chain. In this work, we report the isolation and the characterization, in Escherichia coli, of a novel oligomeric form (alphabeta)2 for A. aeolicus LeuRS, which is present in addition to the alphabeta heterodimer. A. aeolicus (alphabeta)2 LeuRS has been characterized by biochemical and biophysical methods. Native gel electrophoresis, mass spectrometry, analytical ultracentrifugation, and kinetic analysis confirmed that the (alphabeta)2 enzyme was a stable and active entity. By mass spectrometry we confirmed that the heterodimer alphabeta can bind one tRNALeu molecule whereas the heterotetramer (alphabeta)2 can bind two tRNALeu molecules. Active site titration and aminoacylation assays showed that two functional active sites are found per heterotetramer, suggesting that this molecular species might exist and be active in vivo. All those data suggest that the existence of the heterotetramer is certainly not an artifact of overexpression in E. coli. |
Jaeger, S; Martin, F; Rudinger-Thirion, J; Giege, R; Eriani, G Binding of human SLBP on the 3'-UTR of histone precursor H4-12 mRNA induces structural rearrangements that enable U7 snRNA anchoring Article de journal Nucleic Acids Res, 34 (17), p. 4987-4995, 2006, ISBN: 16982637, (1362-4962 (Electronic) Journal Article). Résumé | Liens | BibTeX | Étiquettes: ERIANI, GIEGE ERIANI FRUGIER, Unité ARN @article{, title = {Binding of human SLBP on the 3'-UTR of histone precursor H4-12 mRNA induces structural rearrangements that enable U7 snRNA anchoring}, author = {S Jaeger and F Martin and J Rudinger-Thirion and R Giege and G Eriani}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16982637}, isbn = {16982637}, year = {2006}, date = {2006-01-01}, journal = {Nucleic Acids Res}, volume = {34}, number = {17}, pages = {4987-4995}, abstract = {In metazoans, cell-cycle-dependent histones are produced from poly(A)-lacking mRNAs. The 3' end of histone mRNAs is formed by an endonucleolytic cleavage of longer precursors between a conserved stem-loop structure and a purine-rich histone downstream element (HDE). The cleavage requires at least two trans-acting factors: the stem-loop binding protein (SLBP), which binds to the stem-loop and the U7 snRNP, which anchors to histone pre-mRNAs by annealing to the HDE. Using RNA structure-probing techniques, we determined the secondary structure of the 3'-untranslated region (3'-UTR) of mouse histone pre-mRNAs H4-12, H1t and H2a-614. Surprisingly, the HDE is embedded in hairpin structures and is therefore not easily accessible for U7 snRNP anchoring. Probing of the 3'-UTR in complex with SLBP revealed structural rearrangements leading to an overall opening of the structure especially at the level of the HDE. Electrophoretic mobility shift assays demonstrated that the SLBP-induced opening of HDE actually facilitates U7 snRNA anchoring on the histone H4-12 pre-mRNAs 3' end. These results suggest that initial binding of the SLBP functions in making the HDE more accessible for U7 snRNA anchoring.}, note = {1362-4962 (Electronic) Journal Article}, keywords = {ERIANI, GIEGE ERIANI FRUGIER, Unité ARN}, pubstate = {published}, tppubtype = {article} } In metazoans, cell-cycle-dependent histones are produced from poly(A)-lacking mRNAs. The 3' end of histone mRNAs is formed by an endonucleolytic cleavage of longer precursors between a conserved stem-loop structure and a purine-rich histone downstream element (HDE). The cleavage requires at least two trans-acting factors: the stem-loop binding protein (SLBP), which binds to the stem-loop and the U7 snRNP, which anchors to histone pre-mRNAs by annealing to the HDE. Using RNA structure-probing techniques, we determined the secondary structure of the 3'-untranslated region (3'-UTR) of mouse histone pre-mRNAs H4-12, H1t and H2a-614. Surprisingly, the HDE is embedded in hairpin structures and is therefore not easily accessible for U7 snRNP anchoring. Probing of the 3'-UTR in complex with SLBP revealed structural rearrangements leading to an overall opening of the structure especially at the level of the HDE. Electrophoretic mobility shift assays demonstrated that the SLBP-induced opening of HDE actually facilitates U7 snRNA anchoring on the histone H4-12 pre-mRNAs 3' end. These results suggest that initial binding of the SLBP functions in making the HDE more accessible for U7 snRNA anchoring. |
2005 |
Ryckelynck, M; Masquida, B; Giege, R; Frugier, M An intricate RNA structure with two tRNA-derived motifs directs complex formation between yeast aspartyl-tRNA synthetase and its mRNA Article de journal J Mol Biol, 354 (3), p. 614-629, 2005, ISBN: 16257416, (0022-2836 (Print) Journal Article). Résumé | Liens | BibTeX | Étiquettes: ERIANI, FRUGIER, Messenger/*chemistry/*metabolism RNA, Molecular Molecular Sequence Data Nucleic Acid Conformation Protein Structure, Non-U.S. Gov't Saccharomyces cerevisiae/*enzymology/*genetics Sequence Alignment Sequence Homology, Nucleic Acid Solubility, RYCKELYNCK, Tertiary RNA, Transfer/*chemistry/*metabolism Research Support, Unité ARN, WESTHOF GIEGE FRUGIER Aspartate-tRNA Ligase/genetics/*metabolism Base Sequence DNA Footprinting Gene Deletion Models @article{, title = {An intricate RNA structure with two tRNA-derived motifs directs complex formation between yeast aspartyl-tRNA synthetase and its mRNA}, author = {M Ryckelynck and B Masquida and R Giege and M Frugier}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16257416}, isbn = {16257416}, year = {2005}, date = {2005-01-01}, journal = {J Mol Biol}, volume = {354}, number = {3}, pages = {614-629}, abstract = {Accurate translation of genetic information necessitates the tuned expression of a large group of genes. Amongst them, controlled expression of the enzymes catalyzing the aminoacylation of tRNAs, the aminoacyl-tRNA synthetases, is essential to insure translational fidelity. In the yeast Saccharomyces cerevisiae, expression of aspartyl-tRNA synthetase (AspRS) is regulated in a process necessitating recognition of the 5' extremity of AspRS messenger RNA (mRNA(AspRS)) by its translation product and adaptation to the cellular tRNA(Asp) concentration. Here, we have established the folding of the approximately 300 nucleotides long 5' end of mRNA(AspRS) and identified the structural signals involved in the regulation process. We show that the regulatory region in mRNA(AspRS) folds in two independent and symmetrically structured domains spaced by two single-stranded connectors. Domain I displays a tRNA(Asp) anticodon-like stem-loop structure with mimics of the aspartate identity determinants, that is restricted in domain II to a short double-stranded helix. The overall mRNA structure, based on enzymatic and chemical probing, supports a three-dimensional model where each monomer of yeast AspRS binds one individual domain and recognizes the mRNA structure as it recognizes its cognate tRNA(Asp). Sequence comparison of yeast genomes shows that the features within the mRNA recognized by AspRS are conserved in different Saccharomyces species. In the recognition process, the N-terminal extension of each AspRS subunit plays a crucial role in anchoring the tRNA-like motifs of the mRNA on the synthetase.}, note = {0022-2836 (Print) Journal Article}, keywords = {ERIANI, FRUGIER, Messenger/*chemistry/*metabolism RNA, Molecular Molecular Sequence Data Nucleic Acid Conformation Protein Structure, Non-U.S. Gov't Saccharomyces cerevisiae/*enzymology/*genetics Sequence Alignment Sequence Homology, Nucleic Acid Solubility, RYCKELYNCK, Tertiary RNA, Transfer/*chemistry/*metabolism Research Support, Unité ARN, WESTHOF GIEGE FRUGIER Aspartate-tRNA Ligase/genetics/*metabolism Base Sequence DNA Footprinting Gene Deletion Models}, pubstate = {published}, tppubtype = {article} } Accurate translation of genetic information necessitates the tuned expression of a large group of genes. Amongst them, controlled expression of the enzymes catalyzing the aminoacylation of tRNAs, the aminoacyl-tRNA synthetases, is essential to insure translational fidelity. In the yeast Saccharomyces cerevisiae, expression of aspartyl-tRNA synthetase (AspRS) is regulated in a process necessitating recognition of the 5' extremity of AspRS messenger RNA (mRNA(AspRS)) by its translation product and adaptation to the cellular tRNA(Asp) concentration. Here, we have established the folding of the approximately 300 nucleotides long 5' end of mRNA(AspRS) and identified the structural signals involved in the regulation process. We show that the regulatory region in mRNA(AspRS) folds in two independent and symmetrically structured domains spaced by two single-stranded connectors. Domain I displays a tRNA(Asp) anticodon-like stem-loop structure with mimics of the aspartate identity determinants, that is restricted in domain II to a short double-stranded helix. The overall mRNA structure, based on enzymatic and chemical probing, supports a three-dimensional model where each monomer of yeast AspRS binds one individual domain and recognizes the mRNA structure as it recognizes its cognate tRNA(Asp). Sequence comparison of yeast genomes shows that the features within the mRNA recognized by AspRS are conserved in different Saccharomyces species. In the recognition process, the N-terminal extension of each AspRS subunit plays a crucial role in anchoring the tRNA-like motifs of the mRNA on the synthetase. |
Ryckelynck, M; Giege, R; Frugier, M tRNAs and tRNA mimics as cornerstones of aminoacyl-tRNA synthetase regulations Article de journal Biochimie, 87 (9-10), p. 835-845, 2005, ISBN: 15925436, (0300-9084 Journal article). Résumé | Liens | BibTeX | Étiquettes: ERIANI, FRUGIER, GIEGE FRUGIER, RYCKELYNCK, Unité ARN @article{, title = {tRNAs and tRNA mimics as cornerstones of aminoacyl-tRNA synthetase regulations}, author = {M Ryckelynck and R Giege and M Frugier}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15925436}, isbn = {15925436}, year = {2005}, date = {2005-01-01}, journal = {Biochimie}, volume = {87}, number = {9-10}, pages = {835-845}, abstract = {Structural plasticity of transfer RNA (tRNA) molecules is essential for interactions with their biological partners in aminoacylation reactions and during ribosome-dependent protein synthesis. This holds true when tRNAs are recruited for other functions than translation. Here we review regulation pathways where tRNAs and tRNA mimics play a pivotal role. We further discuss the importance of the identity signals used in aminoacylation that are also required to specify regulatory mechanisms. Such mechanisms are diverse and intervene in transcription, splicing and translation. Altogether, the review highlights the many manners architectural features of tRNA were selected by evolution to control biological key processes.}, note = {0300-9084 Journal article}, keywords = {ERIANI, FRUGIER, GIEGE FRUGIER, RYCKELYNCK, Unité ARN}, pubstate = {published}, tppubtype = {article} } Structural plasticity of transfer RNA (tRNA) molecules is essential for interactions with their biological partners in aminoacylation reactions and during ribosome-dependent protein synthesis. This holds true when tRNAs are recruited for other functions than translation. Here we review regulation pathways where tRNAs and tRNA mimics play a pivotal role. We further discuss the importance of the identity signals used in aminoacylation that are also required to specify regulatory mechanisms. Such mechanisms are diverse and intervene in transcription, splicing and translation. Altogether, the review highlights the many manners architectural features of tRNA were selected by evolution to control biological key processes. |